[gmx-users] writing forces in gromacs

[Amit Choubey]

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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