[gmx-users] the mdp file

[Justin A. Lemkul]

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?

-Justin

> What is the problem?
> 
> Thank you for your reply.
> 
> Yang
> ________________________________________
> 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
> 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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> 
> --
> ========================================
> 
> 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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-- 
========================================

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

========================================