[gmx-users] gmxcheck

[Justin Lemkul]

On 11/4/13 7:37 AM, Ankita Naithani wrote:
> 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?
>

Yes, buried in a long list of other things.  Trivial details like that are 
simply read from the last few lines of the .top though, so there's no need to 
invoke any other accessory programs.

-Justin

>
>
>
> 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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>
>
>

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

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

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