[gmx-users] the mdp file

[Justin A. Lemkul]

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 
circumstances.

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.

-Justin

> 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.
> 
> Yang
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-- 
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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