[gmx-users] Visualizing a process

[Justin Lemkul]

On 8/9/12 2:32 PM, Shima Arasteh wrote:
> 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).
>

An .xtc file is only written if you have nstxtcout set to a non-zero value in 
the .mdp file.  Otherwise, the .trr file is your trajectory in full precision.

-Justin

>
> 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

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