Hi Sangeeta,
Also check whether you have isolated water molecules in your system
(notably the one starting at atom id 13339). If so, that may be a
cause of crash and it would be better just to delete the water
molecule.
Best,
Tsjerk
On 7/3/06, Mark Abraham <[EMAIL PROTECTED]> wrote:
sangeeta wrote:
> I could not mail you as our net was down,
> you asked me "Is your system
> properly minimized? "
> My question is how can I understand whether my system is properly minimised?
Look at the structure before you minimize it, and look at the structure
after you minimize it. See what has changed and use some chemical
judgement. If you're uncertain of yourself, experiment with some smaller
systems before using a system as large as yours.
Mark
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
--
Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
_______________________________________________
gmx-users mailing list gmx-users@gromacs.org
http://www.gromacs.org/mailman/listinfo/gmx-users
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
