[gmx-users] gmxcheck

[Ankita Naithani]

I do have the .mdp file. Main thing I was concerned about were details like
number of water molecules added and number of counter ions added. Does
gmxdump output that information?




On Mon, Nov 4, 2013 at 12:19 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 11/4/13 7:14 AM, Ankita Naithani wrote:
>
>> Hi Justin,
>>
>> Thank you for your reply. I did give the .tpr file but the job terminated
>> after few frames only. Also, if that is not helpful, do you have any
>>
>
> There are no frames in a .tpr file.  I suspect you're simply issuing the
> command incorrectly, but since you haven't shown us what you're doing,
> there's little else to suggest.
>
>
>  suggestions to recover the essential information which you would include
>> as
>> part of methods?
>>
>>
> The .mdp file has all the instructions for the simulation.  If you don't
> have that around for whatever reason (very bad to get rid of such files!),
> all of the same information is recorded in the beginning of the .log file
> or can be written out by gmxdump.  In the latter case, make sure to
> redirect the output to a file rather than just have thousands of lines of
> text blur by in the terminal.
>
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>
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-- 
Ankita Naithani