Hi Berk. Thanks a lot. I did not know that.
Amit On Mon, Feb 22, 2010 at 11:57 PM, Berk Hess <g...@hotmail.com> wrote: > Hi, > > 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. > > Berk > > ------------------------------ > Date: Mon, 22 Feb 2010 23:52:13 -0800 > From: kgp.a...@gmail.com > To: gmx-users@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 = Yo > cpp = /usr/bin/cpp > constraints = none > integrator = md > dt = 0.002 ; ps ! > nsteps = 8500 ; total 17 ps. > nstcomm = 0 > nstxout = 500 > nstvout = 500 > *nstfout = 500* > nstlog = 100 > nstenergy = 10 > nstlist = 10 > ns_type = grid > rlist = 1.3 > coulombtype = Reaction-Field-zero > rcoulomb = 1.0 > epsilon_rf = 0 > vdwtype = Shift > rvdw = 1.0 > rvdw_switch = 0.9 > Tcoupl = no > energygrps = DPPC SOL > Pcoupl = no > gen_vel = no > lincs_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.itp > Opening library file > /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/ffgmxbon.itp > Opening 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 combinations > Opening library file > /home/hpc-23/vedadi/gromacs-4.0.5/tmp/share/gromacs/top/spc.itp > Excluding 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.dat > Making dummy/rest group for T-Coupling containing 1933647 elements > Making dummy/rest group for Acceleration containing 1933647 elements > Making dummy/rest group for Freeze containing 1933647 elements > Making dummy/rest group for VCM containing 1933647 elements > Number of degrees of freedom in T-Coupling group rest is 3924894.00 > Making dummy/rest group for User1 containing 1933647 elements > Making dummy/rest group for User2 containing 1933647 elements > Making dummy/rest group for XTC containing 1933647 elements > Making dummy/rest group for Or. Res. Fit containing 1933647 elements > Making dummy/rest group for QMMM containing 1933647 elements > T-Coupling has 1 element(s): rest > Energy Mon. has 2 element(s): DPPC SOL > 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): rest > Or. Res. Fit has 1 element(s): rest > QMMM 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.<http://windows.microsoft.com/shop> > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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