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 /<ckcu...@umich.edu>/* wrote:
From: kyungchan chae <ckcu...@umich.edu>
Subject: RE: [gmx-users] extending simulations
To: "'Discussion list for GROMACS users'" <gmx-users@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-boun...@gromacs.org
<http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-boun...@gromacs.org>
[mailto:gmx-users-boun...@gromacs.org
<http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-users-boun...@gromacs.org>]
On Behalf Of Anna Marabotti
Sent: Wednesday, May 06, 2009 8:31 AM
To: gmx-users@gromacs.org
<http://in.mc948.mail.yahoo.com/mc/compose?to=gmx-us...@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: amarabo...@isa.cnr.it
<http://in.mc948.mail.yahoo.com/mc/compose?to=amarabo...@isa.cnr.it>
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
____________________________________________________
"If you think you are too small to make a difference, try sleeping
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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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