[gmx-users] how to check the intermediate coordinated even when the simulation is running

Justin Lemkul jalemkul at vt.edu
Fri Nov 9 13:15:06 CET 2012

On 11/9/12 7:06 AM, Kavyashree M wrote:
> Hi ananya,
> You can get the coordinates using trjconv:
> trjconv -f <file.xtc> -s <file.tpr> -o <file.pdb> -b <initial time in ps>
> -e <final time in ps>

This is more easily accomplished with trjconv -dump.  I would also advise making 
a copy of the .trr/.xtc file to be operated upon rather than trying to do I/O 
operations on a file that may be accessed by the simulation while it is running.

> this will give you pdb at the time you have mentioned.
> For your first question- as far as I know you need to check whether
> there is any periodic image violation using g_mindist. Other things
> what you have to check depends on the parameter you want to see.

It depends on what the OP means by "running properly."  If one simply wants to 
ensure that the simulation is indeed going along, simply listing the files and 
looking at time stamps should tell you that, or following the content of the 
.log file using the Unix command "tail."


> Probably others may give a better answer regarding this.
> Bye
> kavya
> On Fri, Nov 9, 2012 at 5:04 PM, ananyachatterjee <
> ananyachatterjee at iiserkol.ac.in> wrote:
>> I am very new to this MD simulation, by reading the tutorials in the
>> website I have run an simulation and it is running from last 5 day and I am
>> not getting whether it is running properly or not. Could any one kindly
>> tell me how to see whether the simulation is running or not and also how
>> can I check the intermediate coordinated even when the simulation is
>> running. Kindly help me.
>> --
>> Ananya Chatterjee,
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/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/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list