[gmx-users] force
Florian Dommert
dommert at icp.uni-stuttgart.de
Sun Jun 28 12:23:00 CEST 2009
* 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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>
>
>
>--
>Shuangxing Dai
>_______________________________________________
>gmx-users mailing list gmx-users at gromacs.org
>http://lists.gromacs.org/mailman/listinfo/gmx-users
>Please search the archive at http://www.gromacs.org/search before posting!
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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
!! PGP-ENCODED emails preferred !!
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