Версія даної теми для друку

Remmer, дают задания? Три человека всего в команде - присоединяться к проекту не дают ((

Посчитайте кто-нить...

<core_client_version>6.4.5</core_client_version>
<![CDATA[
<stderr_txt>
wrapper: starting
wrapper: running ../../projects/hydrogenathome.org/unzip_1.19_windows_intelx86.exe (-qq -n gromacs.zip)
wrapper: running gromacs/bin/pdb2gmx.exe (-ff amber03 -water tip4p -o conf.gro)
:-) G R O M A C S (-:

Gromacs Runs One Microsecond At Cannonball Speeds

:-) VERSION 4.0.3 (-:


Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright © 1991-2000, University of Groningen, The Netherlands.
Copyright © 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) gromacs/bin/pdb2gmx (-:

Option Filename Type Description
------------------------------------------------------------
-f eiwit.pdb Input Structure file: gro g96 pdb tpr tpb tpa
-o conf.gro Output Structure file: gro g96 pdb
-p topol.top Output Topology file
-i posre.itp Output Include file for topology
-n clean.ndx Output, Opt. Index file
-q clean.pdb Output, Opt. Structure file: gro g96 pdb

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]merge bool no Merge chains into one molecule definition
-ff string amber03 Force field, interactive by default. Use -h for
information.
-water enum tip4p Water model to use: with GROMOS we recommend SPC,
with OPLS, TIP4P: spc, spce, tip3p, tip4p, tip5p
or f3c
-[no]inter bool no Set the next 8 options to interactive
-[no]ss bool no Interactive SS bridge selection
-[no]ter bool no Interactive termini selection, iso charged
-[no]lys bool no Interactive Lysine selection, iso charged
-[no]arg bool no Interactive Arganine selection, iso charged
-[no]asp bool no Interactive Aspartic Acid selection, iso charged
-[no]glu bool no Interactive Glutamic Acid selection, iso charged
-[no]gln bool no Interactive Glutamine selection, iso neutral
-[no]his bool no Interactive Histidine selection, iso checking
H-bonds
-angle real 135 Minimum hydrogen-donor-acceptor angle for a
H-bond (degrees)
-dist real 0.3 Maximum donor-acceptor distance for a H-bond (nm)
-[no]una bool no Select aromatic rings with united CH atoms on
Phenylalanine, Tryptophane and Tyrosine
-[no]ignh bool no Ignore hydrogen atoms that are in the pdb file
-[no]missing bool no Continue when atoms are missing, dangerous
-[no]v bool no Be slightly more verbose in messages
-posrefc real 1000 Force constant for position restraints
-vsite enum none Convert atoms to virtual sites: none, hydrogens
or aromatics
-[no]heavyh bool no Make hydrogen atoms heavy
-[no]deuterate bool no Change the mass of hydrogens to 2 amu

Opening library file ffamber03.rtp
Opening library file aminoacids.dat
Opening library file aminoacids.dat
Opening library file atommass.dat
Opening library file vdwradii.dat
Opening library file dgsolv.dat
Opening library file electroneg.dat
Opening library file elements.dat
Opening library file xlateat.dat
26 out of 26 lines of xlateat.dat converted succesfully
WARNING: there were 1851 atoms with zero occupancy and 16 atoms with
occupancy unequal to one (out of 1868 atoms). Check your pdb file.
Opening library file ffamber03.atp

Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Atomtype 1
Opening library file ffamber03.rtp

Residue 1
Residue 2
Residue 3
Residue 4
Residue 5
Residue 6
Residue 7
Residue 8
Residue 9
Residue 10
Residue 11
Residue 12
Residue 13
Residue 14
Residue 15
Residue 16
Residue 17
Residue 18
Residue 19
Residue 20
Residue 21
Residue 22
Residue 23
Residue 24
Residue 25
Residue 26
Residue 27
Residue 28
Residue 29
Residue 30
Residue 31
Residue 32
Residue 33
Residue 34
Residue 35
Residue 36
Residue 37
Residue 38
Residue 39
Residue 40
Residue 41
Residue 42
Residue 43
Residue 44
Residue 45
Residue 46
Residue 47
Residue 48
Residue 49
Residue 50
Residue 51
Residue 52
Residue 53
Residue 54
Residue 55
Residue 56
Residue 57
Residue 58
Residue 59
Residue 60
Residue 61
Residue 62
Residue 63
Residue 64
Residue 65
Residue 66
Residue 67
Residue 68
Residue 69
Residue 70
Residue 71
Residue 72
Residue 73
Residue 74
Residue 75
Residue 76
Residue 77
Residue 78
Residue 79
Residue 80
Residue 81
Residue 82
Residue 83
Residue 84
Residue 85
Residue 86
Residue 87
Residue 88
Residue 89
Residue 90
Residue 91
Residue 92
Residue 93
Residue 94
Residue 95
Residue 96
Residue 97
Residue 98
Residue 99
Residue 100
Residue 101
Residue 102
Residue 103
Residue 104
Residue 105
Residue 106
Residue 107
Residue 108
Residue 109
Residue 110
Residue 111
Residue 112
Residue 113
Residue 114
Residue 115
Residue 116
Residue 117
Residue 118
Residue 119
Residue 120
Residue 121
Residue 122
Residue 123
Residue 124
Residue 125
Residue 126
Residue 127
Residue 128
Residue 129
Residue 130
Residue 131
Sorting it all out...
Opening library file ffamber03.hdb
Opening library file ffamber03-n.tdb
Opening library file ffamber03-c.tdb
There are 342 donors and 342 acceptors
There are 427 hydrogen bonds
Opening library file specbond.dat
7 out of 7 lines of specbond.dat converted succesfully
Special Atom Distance matrix:
MET22 MET60 MET90 MET142 MET180
SD168 SD469 SD695 SD1101 SD1402
MET60 SD469 1.198
MET90 SD695 2.273 1.291
MET142 SD1101 3.755 3.577 4.559
MET180 SD1402 3.688 3.217 3.924 1.222
MET210 SD1628 4.989 4.300 4.652 2.507 1.520
Making bonds...
Warning: Long Bond (1-5 = 0.458477 nm)
Warning: Long Bond (5-7 = 0.365351 nm)
Warning: Long Bond (5-18 = 0.286245 nm)
Warning: Long Bond (7-10 = 0.250088 nm)
Warning: Long Bond (10-11 = 0.510701 nm)
Warning: Long Bond (10-16 = 0.583405 nm)
Warning: Long Bond (11-12 = 0.951967 nm)
Warning: Long Bond (14-16 = 0.336489 nm)
Warning: Long Bond (18-19 = 0.330189 nm)
Warning: Long Bond (18-20 = 8.76171 nm)
Warning: Long Bond (18-20 = 8.76171 nm)
Warning: Short Bond (281-282 = 0.0173118 nm)
Warning: Short Bond (1223-1224 = 0.03919 nm)
Warning: Long Bond (1836-1840 = 0.375255 nm)
Warning: Long Bond (1840-1842 = 0.565792 nm)
Warning: Long Bond (1840-1853 = 0.608461 nm)
Warning: Long Bond (1842-1845 = 0.300082 nm)
Warning: Long Bond (1845-1846 = 1.06587 nm)
Warning: Long Bond (1845-1851 = 0.809173 nm)
Warning: Long Bond (1846-1847 = 0.905759 nm)
Warning: Long Bond (1847-1849 = 0.422019 nm)
Warning: Long Bond (1849-1851 = 0.501367 nm)
Warning: Long Bond (1853-1854 = 0.675574 nm)
Warning: Long Bond (1853-1855 = 7.24217 nm)
Warning: Long Bond (1853-1855 = 7.24217 nm)
Warning: Short Bond (3309-3310 = 0.0469252 nm)
Warning: Short Bond (3309-3311 = 0.0473808 nm)
Warning: Short Bond (3441-3442 = 0.0498146 nm)
Warning: Short Bond (3441-3443 = 0.0371581 nm)
Opening library file aminoacids.dat
Number of bonds was 3720, now 3718
Generating angles, dihedrals and pairs...
Before cleaning: 9746 pairs
Before cleaning: 9886 dihedrals
Keeping all generated dihedrals
There are 9886 dihedrals, 745 impropers, 6740 angles
9680 pairs, 3718 bonds and 0 virtual sites
Total mass 26734.992 a.m.u.
Total charge -4.000 e
Writing topology

Writing coordinate file...
wrapper: running gromacs/bin/grompp.exe (-f grompp_min.mdp -c conf.gro)
Option Filename Type Description
------------------------------------------------------------
-f grompp_min.mdp Input, Opt! grompp input file with MD parameters
-po mdout.mdp Output grompp input file with MD parameters
-c conf.gro Input Structure file: gro g96 pdb tpr tpb tpa
-r conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-rb conf.gro Input, Opt. Structure file: gro g96 pdb tpr tpb tpa
-n index.ndx Input, Opt. Index file
-p topol.top Input Topology file
-pp processed.top Output, Opt. Topology file
-o topol.tpr Output Run input file: tpr tpb tpa
-t traj.trr Input, Opt. Full precision trajectory: trr trj cpt
-e ener.edr Input, Opt. Energy file: edr ene

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-[no]v bool yes Be loud and noisy
-time real -1 Take frame at or first after this time.
-[no]rmvsbds bool yes Remove constant bonded interactions with virtual
sites
-maxwarn int 0 Number of allowed warnings during input processing
-[no]zero bool no Set parameters for bonded interactions without
defaults to zero instead of generating an error
-[no]renum bool yes Renumber atomtypes and minimize number of
atomtypes

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
checking input for internal consistency...
Generated 2701 of the 2701 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 2701 of the 2701 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein'

NOTE 1 [file topol.top, line 34498]:
System has non-zero total charge: -4.000002e+00



processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Opening library file aminoacids.dat
Making dummy/rest group for T-Coupling containing 3670 elements
Making dummy/rest group for Acceleration containing 3670 elements
Making dummy/rest group for Freeze containing 3670 elements
Making dummy/rest group for VCM containing 3670 elements
Number of degrees of freedom in T-Coupling group rest is 11007.00
Making dummy/rest group for User1 containing 3670 elements
Making dummy/rest group for User2 containing 3670 elements
Making dummy/rest group for Or. Res. Fit containing 3670 elements
Making dummy/rest group for QMMM containing 3670 elements
T-Coupling has 1 element(s): rest
Energy Mon. has 1 element(s): Protein
Acceleration has 1 element(s): rest
Freeze has 1 element(s): rest
User1 has 1 element(s): rest
User2 has 1 element(s): rest
VCM has 1 element(s): rest
XTC has 1 element(s): Protein
Or. Res. Fit has 1 element(s): rest
QMMM has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 2 [file grompp_min.mdp, line unknown]:
You are using a plain Coulomb cut-off, this will often produce artifacts.
You might want to consider using PME electrostatics.


writing run input file...

There were 2 notes

gcq#185: "It is Lunchtime" (A.R. Van Buuren)

wrapper: running gromacs/bin/mdrun.exe ()
:-) G R O M A C S (-:

Great Red Owns Many ACres of Sand

:-) VERSION 4.0.3 (-:


Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright © 1991-2000, University of Groningen, The Netherlands.
Copyright © 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) gromacs/bin/mdrun (-:

Option Filename Type Description
------------------------------------------------------------
-s topol.tpr Input Run input file: tpr tpb tpa
-o traj.trr Output Full precision trajectory: trr trj cpt
-x traj.xtc Output, Opt. Compressed trajectory (portable xdr format)
-cpi state.cpt Input, Opt. Checkpoint file
-cpo state.cpt Output, Opt. Checkpoint file
-c confout.gro Output Structure file: gro g96 pdb
-e ener.edr Output Energy file: edr ene
-g md.log Output Log file
-dgdl dgdl.xvg Output, Opt. xvgr/xmgr file
-field field.xvg Output, Opt. xvgr/xmgr file
-table table.xvg Input, Opt. xvgr/xmgr file
-tablep tablep.xvg Input, Opt. xvgr/xmgr file
-tableb table.xvg Input, Opt. xvgr/xmgr file
-rerun rerun.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi tpi.xvg Output, Opt. xvgr/xmgr file
-tpid tpidist.xvg Output, Opt. xvgr/xmgr file
-ei sam.edi Input, Opt. ED sampling input
-eo sam.edo Output, Opt. ED sampling output
-j wham.gct Input, Opt. General coupling stuff
-jo bam.gct Output, Opt. General coupling stuff
-ffout gct.xvg Output, Opt. xvgr/xmgr file
-devout deviatie.xvg Output, Opt. xvgr/xmgr file
-runav runaver.xvg Output, Opt. xvgr/xmgr file
-px pullx.xvg Output, Opt. xvgr/xmgr file
-pf pullf.xvg Output, Opt. xvgr/xmgr file
-mtx nm.mtx Output, Opt. Hessian matrix
-dn dipole.ndx Output, Opt. Index file

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-[no]sum bool yes Sum the energies at every step
-[no]v bool no Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 15 Checkpoint interval (minutes)
-[no]append bool no Append to previous output files when restarting
from checkpoint
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system

Reading file topol.tpr, VERSION 4.0.3 (single precision)
Steepest Descents:
Tolerance (Fmax) = 1.00000e+00
Number of steps = 2000
Warning: 1-4 interaction between 1 and 20 at distance 8.662 which is larger than the 1-4 table size 2.000 nm
These are ignored for the rest of the simulation
This usually means your system is exploding,
if not, you should increase table-extension in your mdp file
or with user tables increase the table size

Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precision Fmax < 1

Double precision normally gives you higher accuracy.

writing lowest energy coordinates.

Steepest Descents converged to machine precision in 550 steps,
but did not reach the requested Fmax < 1.
Potential Energy = 7.3886250e+04
Maximum force = 3.1850342e+03 on atom 2895
Norm of force = 3.1263608e+02

gcq#151: "I Ripped the Cord Right Out Of the Phone" (Capt. Beefheart)

called boinc_finish

</stderr_txt>
]]>

я скачал ВУ из интернета, она мне оказалась не нужна, как мне закачать её обратно?

01.05.2009 23:15:54 Hydrogen@Home [error] Error reported by file upload server: Server is out of disk space

2009-12-17: Send a message to ZPM regarding credit restores

http://hydrogenathome.org/forum_thread.php?id=430 список по нашей команде. Ждите пополнение счета

фсьо уже (((

Получил одну ВЮ

больше нет

Не калорийный проект - 21к секунд за 64 очка...

Были задания

в одиночку тяжко команду тянуть
или все хотят парами бензина дышать и т.д. ?

Да, пары водорода зло, особенно оксиды. Разъедают все подряд Если такие вещества попадут в руки террористов, то всем хана!

я на двух ядерке сижу
3 проекта основных и + HYDROGEN
и от 60 до 400 выдаю
булоб бажання

и какие приоритеты у 3 проектов и водорода? какие настройки кэша? мне в день одно задание __иногда__ перепадает на 2-ядерном ноуте

добавил проект на 3 виртуалки на той же машине. посмотрим на прирост улова ВЮ

Test3 is a success, were going to push forward and move on.

we officially have a working cuda app.

we now need to integrate, checkpoint, and get progress bar working.

i'll keep this up-to-date as much as i can.

--
Tim Turner
http://hydrogenathome.org/forum_thread.php?id=434

John Shultz has sent you a message.
Date: 9/17/2011
Subject: RE: hi, hydrogen@home
Hi Dimitriy,

I've lost interest in this project. I'm not preparing to send any work out.

балбес.

попросил его официально об этом написать в новостях проекта