[gmx-users] force

[Shuangxing Dai]

Yes, they are all zeros. I am confused why this happen. Thank you for help.
And here is the mdp file:
; RUN CONTROL PARAMETERS =
integrator               = steep
nsteps                   = 50
; Output frequency for coords (x), velocities (v) and forces (f)
nstxout                  = 1
nstvout                  = 1
nstfout                  = 1
; Output frequency for energies to log file and energy file
nstlog                   = 1
nstenergy                = 1
; Output frequency and precision for xtc file
nstxtcout                = 1
xtc-precision            = 1000
; ENERGY MINIMIZATION OPTIONS =
; Force tolerance and initial step-size =
emtol                    = 1
emstep                   = 0.01
; NEIGHBORSEARCHING PARAMETERS =
; nblist update frequency =
nstlist                  =3
; ns algorithm (simple or grid) =
ns_type                  = simple
; Periodic boundary conditions: xyz or none =
pbc                      = xyz
; nblist cut-off         =
rlist                    =0.9
; OPTIONS FOR ELECTROSTATICS AND VDW =
; Method for doing electrostatics =
coulombtype              = Shift
rcoulomb                 = 0.9
; Dielectric constant (DC) for cut-off or DC of reaction field =
epsilon-r                = 1
; Method for doing Van der Waals =
vdw-type                 = Cut-off
; cut-off lengths        =
rvdw                     = 0.9
; Spacing for the PME/PPPM FFT grid =
fourierspacing           = 0.1
; FFT grid size, when a value is 0 fourierspacing will be used =
fourier_nx               = 0
fourier_ny               = 0
fourier_nz               = 0
; EWALD/PME/PPPM parameters =
pme_order                = 6
ewald_rtol               = 1e-05
epsilon_surface          = 0
optimize_fft             = no

And also another question, can Gromacs write out the energy for each atom at
each step? Just like it did to the forces? I use this mdp file and only see
the total energy for each step in the log file.
Thanks again.

On Sat, Jun 27, 2009 at 8:07 PM, Florian Dommert <
dommert at icp.uni-stuttgart.de> wrote:

> * Shuangxing Dai <shuangxingdai at gmail.com> [2009-06-27 18:57:41 -0600]:
>
>  The nstfout =1 in mdout.mdp. So this should not be where the problem is.
>>
>
> So this was the most obvious mistake I could imagine and you see it is
> always appreciated that you put your mdp file also to the list, that
> everybody knows your input parameters. However in case you already told
> gromacs to write out the data to the trr file it should be there.
> So if you try:
>
>  echo 0 | g_traj -f traj.trr -s topol.tpr -of
> Only zeros are contained in force.xvg ??
>
> /Flo
>
>
>
>> ----- Original Message ----- From: "Florian Dommert" <
>> dommert at icp.uni-stuttgart.de>
>> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>> Sent: Saturday, June 27, 2009 3:20 PM
>> Subject: Re: [gmx-users] force
>>
>>
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>
> --
> Florian Dommert
> Dipl.-Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
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-- 
Shuangxing Dai
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