[gmx-users] writing forces in gromacs
gmx3 at hotmail.com
Tue Feb 23 08:57:47 CET 2010
This note is printed when output files will be "large", large is defined as more than 2 GB.
Not writing forces just gets you under this limit.
Date: Mon, 22 Feb 2010 23:52:13 -0800
From: kgp.amit at gmail.com
To: gmx-users at gromacs.org
Subject: [gmx-users] writing forces in gromacs
I had been trying to work with forces of the atoms and stumbled upon something weird.
In my md.mdp file i ask to write forces with a certain frequency then the grompp shows a seemingly harmless note, the full md.mdp and extract of the grompp.out are as follows :-
title = Yocpp = /usr/bin/cppconstraints = noneintegrator = mddt = 0.002 ; ps !
nsteps = 8500 ; total 17 ps.nstcomm = 0nstxout = 500nstvout = 500
nstfout = 500nstlog = 100nstenergy = 10nstlist = 10ns_type = gridrlist = 1.3
coulombtype = Reaction-Field-zerorcoulomb = 1.0epsilon_rf = 0
vdwtype = Shiftrvdw = 1.0rvdw_switch = 0.9
Tcoupl = noenergygrps = DPPC SOLPcoupl = nogen_vel = nolincs_iter = 2
Ignoring obsolete mdp entry 'title'Ignoring obsolete mdp entry 'cpp'checking input for internal consistency...Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmx.itp
Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxnb.itpOpening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxbon.itpOpening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ff_dum.itp
Generated 1369 of the 2211 non-bonded parameter combinationsOpening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/spc.itpExcluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'processing coordinates...double-checking input for internal consistency...renumbering atomtypes...converting bonded parameters...
initialising group options...processing index file...Opening library file /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/aminoacids.datMaking dummy/rest group for T-Coupling containing 1933647 elements
Making dummy/rest group for Acceleration containing 1933647 elementsMaking dummy/rest group for Freeze containing 1933647 elementsMaking dummy/rest group for VCM containing 1933647 elements
Number of degrees of freedom in T-Coupling group rest is 3924894.00Making dummy/rest group for User1 containing 1933647 elementsMaking dummy/rest group for User2 containing 1933647 elements
Making dummy/rest group for XTC containing 1933647 elementsMaking dummy/rest group for Or. Res. Fit containing 1933647 elementsMaking dummy/rest group for QMMM containing 1933647 elements
T-Coupling has 1 element(s): restEnergy Mon. has 2 element(s): DPPC SOLAcceleration has 1 element(s): restFreeze has 1 element(s): restUser1 has 1 element(s): rest
User2 has 1 element(s): restVCM has 1 element(s): restXTC has 1 element(s): restOr. Res. Fit has 1 element(s): restQMMM has 1 element(s): rest
Checking consistency between energy and charge groups...
NOTE 1 [file nve.mdp, line unknown]: This run will generate roughly 2493 Mb of data
writing run input file...
There was 1 note
gcq#197: "I Do It All the Time" (Magnapop)
:-) G R O M A C S (-:
Now when i change nstfout to zero (no printing of forces) the note doesnt show up anymore.
Also for the case with nstfout = 500 it seems that the forces are being read and written properly, I tried the g_traj tool to see the forces.
Could someone clarify?
Thank you,Amit Choubey
New Windows 7: Simplify what you do everyday. Find the right PC for you.
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