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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