[gmx-users] Visualizing a process

[Shima Arasteh]

OK, I got it. But how can I get a .xtc output of NPT or NVT equilibration? The output of  mdrun -deffnm npt doesn't have any .xtc files to visualize by VMD. I have seen that I get .xtc file just after the final mdrun -deffnm md (as you said).

 
Sincerely,
Shima


----- Original Message -----
From: Justin Lemkul <jalemkul at vt.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: 
Sent: Thursday, August 9, 2012 10:52 PM
Subject: Re: [gmx-users] Visualizing a process



On 8/9/12 2:21 PM, Shima Arasteh wrote:
>
>
>   You mean I can not see the NPT equilibration process!
>

I mean exactly what I said.  You can load the .xtc file as data for a coordinate 
file in, e.g. VMD, and watch the movie of the simulation after it is complete.

-Justin

>
> Sincerely,
> Shima
>
>
> ----- Original Message -----
> From: Justin Lemkul <jalemkul at vt.edu>
> To: Shima Arasteh <shima_arasteh2001 at yahoo.com>; Discussion list for GROMACS users <gmx-users at gromacs.org>
> Cc:
> Sent: Thursday, August 9, 2012 10:45 PM
> Subject: Re: [gmx-users] Visualizing a process
>
>
>
> On 8/9/12 2:12 PM, Shima Arasteh wrote:
>> Hi,
>>
>> Is it possible to view the process of a NPT or NVT equilibration? Which command in gromacs can generate a .xtc output?
>>
>
> Only mdrun writes .xtc files of simulations.  As far as I know, one cannot watch the simulation in real time but .xtc files can be visualized in a variety of viewing programs after the simulation is complete.
>
> -Justin
>
> -- ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
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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