[gmx-users] extending simulations
Justin A. Lemkul
jalemkul at vt.edu
Wed May 6 16:51:02 CEST 2009
Please start a new thread if you are asking a new question; it will help get the
attention of someone who may be interested in helping you, but who may not have
any comments on the "extending simulations" thread.
vidhya sankar wrote:
> dear sir/Madam
>
> i want to work in mopac/gromacs interface for that i have downloaded
> mopac 7-1.10 tar.gz when run ./configure in the TAR file in command
> prompt of redhat linux EL5 to install mopac
>
> i got the the following error in command prompt
>
> *bash: ./configure: /bin/sh^M: bad interpreter: No such file or directory*
>
The configure file has been modified by an editor that has left hidden
characters (^M) at the end of lines. You may need to run something like
dos2unix on the file, or at least explore it (and perhaps others) with a plain
text editor like vi or emacs.
-Justin
> please kindly rectify the error in the configure file i am waiting for
> your reply
>
> thanks in Advance
>
>
>
>
>
>
>
>
>
>
>
> --- On *Wed, 6/5/09, kyungchan chae /<ckcumaa at umich.edu>/* wrote:
>
>
> From: kyungchan chae <ckcumaa at umich.edu>
> Subject: RE: [gmx-users] extending simulations
> To: "'Discussion list for GROMACS users'" <gmx-users at gromacs.org>
> Date: Wednesday, 6 May, 2009, 8:02 PM
>
> If you want to extend your simulation, simply use the 'append' command.
>
> : mdrun -append yes -cpi state.cpt
>
> Extending a simulation is quite simple. However, if your trajectory
> file is
> larger than 2GB, you are going to have a problem. I tested it a few
> weeks
> ago and found out that the 'append' option only worked when the size of
> trajectory file is smaller than 2GB. I reported this issue to Gromacs
> bugzilla(#315). Please check my bug report. I really hope to share
> information about this issue.
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> <http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-bounces@gromacs.org>
> [mailto:gmx-users-bounces at gromacs.org
> <http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-bounces@gromacs.org>]
> On Behalf Of Anna Marabotti
> Sent: Wednesday, May 06, 2009 8:31 AM
> To: gmx-users at gromacs.org
> <http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users@gromacs.org>
> Subject: [gmx-users] extending simulations
>
> Dear all,
> I'd need to have a clarification about how to extend a simulation
> made using
> GROMACS 4 that has been
> interrupted on a system due to walltime expiration. On the Wiki
> section I
> see:
> "A simulation that has completed is extended using tpbconv, mdrun and
> checkpoint files (.cpt). A simulation
> that has terminated, but not completed, due to e.g. the queue time
> ending,
> or better: the use of the -maxh
> option of mdrun, can be continued without tpbconv. First the number
> of steps
> or time has to be changed in the
> .tpr file, then the simulation is continued from the last checkpoint
> with
> mdrun. This will produce a binary
> identical simulation that will be the same as it a continuous run
> was made.
> tpbconv -s previous.tpr -extend timetoextendby -o next.tpr
> mdrun -s next.tpr -cpi previous.cpt"
>
> If I understand well, the procedure using tpbconv should be applied
> only if
> I have finished my previous run
> of, say, 10 ns, and I want to extend it to 20 ns. ONLY in this case
> I have
> to use tpbconv and then mdrun. On
> the contrary, if my run of 10 ns has been interrupted e.g. at 7 ns,
> the only
> command I should provide is:
>
> mdrun -s previous.tpr -cpi previous.cpt
>
> without modifying the previous.tpr file.
> Could you please confirm me about this point?
> Many thanks and best regards
> Anna
>
> ______________________________________________
> Anna Marabotti, Ph.D.
> Laboratory of Bioinformatics and Computational Biology
> Institute of Food Science, CNR
> Via Roma 64
> 83100 Avellino (Italy)
> Phone: +39 0825 299651
> Fax: +39 0825 781585
> Skype: annam1972
> E-mail: amarabotti at isa.cnr.it
> <http://in.mc948.mail.yahoo.com/mc/compose?to=amarabotti@isa.cnr.it>
> Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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