[gmx-users] the mdp file
Justin A. Lemkul
jalemkul at vt.edu
Wed Nov 5 03:54:43 CET 2008
He, Yang wrote:
> Hi Justin,
> I have changed the value of nsteps(>100) and the nstout(=1), but I found that there is just the static figure and no animation .
What are you using for visualization?
> it always shows that :Last frame 0 time 0.000
What tool are you using that is showing this?
> What is the problem?
> Thank you for your reply.
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: Monday, November 03, 2008 4:22 PM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] the mdp file
> He, Yang wrote:
>> Hi all users,
>> When I change the value of nsteps in my mdp file to run the gromacs and show the trajectory in the gromcas, I found that only the value of nsteps is set by 10, is there just the animation of the molecule's movement . I have tried many time and set the other values of nsteps, there isn't any movement about the molecule at all.
> I'm not quite clear on what the problem is. But you should be aware that 10
> steps (0.02 ps in your case!) is an exceedingly short timeframe under any
> If what you've shown is your full .mdp file, then the other values will be taken
> as default. For output (nstxout) this value is 100. So you will likely only
> see the starting and ending coordinates of your 10-step simulation.
> Try a longer simulation (>100 steps) or specify nstxout = 1 and see if you
> generate 10 frames.
>> I am strange about that and this is my part of mdp file:
>> ;VARIOUS PREPROCESSING OPTIONS
>> title = atom
>> ; Preprocessor - specify a full path if necessary.
>> cpp = cpp
>> define =
>> ; RUN CONTROL PARAMETERS
>> integrator = md
>> ; Start time and timestep in ps
>> tinit = 0
>> dt = 0.002
>> nsteps = 10
>> ; For exact run continuation or redoing part of a run
>> init_step = 0
>> ; mode for center of mass motion removal
>> comm-mode = Linear
>> ; number of steps for center of mass motion removal
>> nstcomm = 1
>> ; group(s) for center of mass motion removal
>> comm-grps =
>> ; NEIGHBORSEARCHING PARAMETERS
>> ; nblist update frequency
>> nstlist = 1
>> ; ns algorithm (simple or grid)c 4
>> ns_type = grid
>> ; Periodic boundary conditions: xyz (default), no (vacuum)
>> ; or full (infinite systems only)
>> pbc = xyz
>> ; nblist cut-off
>> rlist = 0.686
>> domain-decomposition = no
>> ; OPTIONS FOR ELECTROSTATICS AND VDW
>> ; Method for doing electrostatics
>> coulombtype = User
>> rcoulomb-switch = 0
>> rcoulomb = 0.9
>> ; Relative dielectric constant for the Cut-off or DC of the reaction field
>> epsilon-r = 78
>> ; Method for doing Van der Waals
>> vdw-type = User
>> ; cut-off lengths
>> rvdw-switch = 0
>> rvdw = 0.9
>> ; Apply long range dispersion corrections for Energy and Pressure
>> DispCorr = EnerPres
>> ; Extension of the potential lookup tables beyond the cut-off
>> table-extension = 1
>> ; Seperate tables between energy group pairs
>> energygrp_table =
>> ; Spacing for the PME/PPPM FFT grid
>> fourierspacing = 0.12
>> ; 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 = 4
>> ewald_rtol = 1e-05
>> ewald_geometry = 3d
>> epsilon_surface = 0
>> optimize_fft = no
>> Can anyone of you tell me what is the problem?
>> Thank you very much.
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> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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