[gmx-users] writing forces in gromacs

[Amit Choubey]

Hi Berk.

Thanks a lot. I did not know that.

Amit

On Mon, Feb 22, 2010 at 11:57 PM, Berk Hess <gmx3 at 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.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               =  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
>
>
> ------------------------------
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