[gmx-users] reg MOPAC/gromacs installations

Sun May 10 17:13:29 CEST 2009

Dear sir/Madam   thanks in Advance                        i Did dos2unixconversions. as u saiid . but still i get error when i run the same output configure in command prompt of Redhat linux5 as followschecking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
: command not foundissing: line 3: 
: command not foundissing: line 5: 
: command not foundissing: line 9: 
: command not foundissing: line 14: 
: command not foundissing: line 19: 
: command not foundissing: line 24: 
: command not foundissing: line 29: 
'root/mopac7-1.10/missing: line 47: syntax error near unexpected token `in
'root/mopac7-1.10/missing: line 47: `case "$1" in
configure: WARNING: `missing' script is too old or missing
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
can not run ./config        /bin/sh  :Error
Please kindly mail me the error free configure file to My personal  Email (scvsankar_agr at yahoo.com)  i am expecting your positive reply if u send me the the  configure file it will be very very helpful to me  thanks in Advance

--- On Wed, 6/5/09, vidhya sankar <scvsankar_agr at yahoo.com> wrote:

From: vidhya sankar <scvsankar_agr at yahoo.com>
Subject: RE: [gmx-users] extending simulations
To: gmx-users at gromacs.org
Date: Wednesday, 6 May, 2009, 8:15 PM

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 
 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 [mailto:gmx-users-bounces at gromacs.org]
On Behalf Of Anna
 Marabotti
Sent: Wednesday, May 06, 2009 8:31 AM
To: gmx-users at 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
Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm
____________________________________________________
"If you think you are too small to make a difference, try sleeping with a
mosquito"

_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests
 to the list. Use the 
www interface or send it to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

_______________________________________________
gmx-users mailing list    gmx-users at gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it
 to gmx-users-request at gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php

       Now surf faster and smarter ! Check out the new Firefox 3 - Yahoo! Edition *  Click here!

      Bollywood news, movie reviews, film trailers and more! Go to http://in.movies.yahoo.com/
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090510/d166b264/attachment.html>