[gmx-users] writing forces in gromacs

Berk Hess 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

Hi everyone,
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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