[gmx-users] gmxcheck

[Ankita Naithani]

Thanks Justin very much for your help. (Extremely silly and unthoughtful of
me to forget this)


Kind regards,

Ankita


On Mon, Nov 4, 2013 at 12:40 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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
>
> ==================================================
> --
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>



-- 
Ankita Naithani