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 <jalem...@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
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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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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