[gmx-users] force

Shuangxing Dai shuangxingdai at gmail.com
Sun Jun 28 20:52:47 CEST 2009 

Yes, I did one md step and got all non-zero forces.
But for the energy minimization, all the forces are zero, althouth mdrun
command gives non-zero forces.

On Sun, Jun 28, 2009 at 4:23 AM, Florian Dommert <
dommert at icp.uni-stuttgart.de> wrote:

> * Shuangxing Dai <shuangxingdai at gmail.com> [2009-06-27 20:22:13 -0600]:
>
>  Yes, they are all zeros. I am confused why this happen. Thank you for
>> help.
>> And here is the mdp file:
>>
>
> That would confuse me, too. As I have never analyzed forces from a
> energy minimization, perhaps there is the problem. Try a zero-step md,
> meaning integrator=md and nsteps=0 and leave the further parameters
> unchanged. In case you get forces in your analysis then, we have
> discovered the source of error :)
>
> /Flo
>
>  ; 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
>>>
>>> Pfaffenwaldring 27
>>> 70569 Stuttgart
>>>
>>> Tel: +49 - 711 / 6856-3613
>>> Fax: +49 - 711 / 6856-3658
>>>
>>> EMail: dommert at icp.uni-stuttgart.de
>>> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert<http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert>
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>>>
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>>
>>
>> --
>> Shuangxing Dai
>>
>
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>
> --
> Florian Dommert
> Dipl.-Phys.
>
> Institute for Computational Physics
> University Stuttgart
>
> Pfaffenwaldring 27
> 70569 Stuttgart
>
> Tel: +49 - 711 / 6856-3613
> Fax: +49 - 711 / 6856-3658
>
> EMail: dommert at icp.uni-stuttgart.de
> Home: http://www.icp.uni-stuttgart.de/~icp/Florian_Dommert<http://www.icp.uni-stuttgart.de/%7Eicp/Florian_Dommert>
>
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>
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-- 
Shuangxing Dai
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