Alok wrote:
@Mark:
Thanks a lot for your reply/comments and time. I am using TIP4P water
model, and I really could not understand why it happens, Some of the
bonds of the water molecules are broken down, and after 1ps MD they
make bonds again. Is it not very strange?
No. Your visual representation "makes" bonds, not the simulation. The
simulation can move the interatomic distances so that the heuristic no
longer detects bonds, and this is what we're trying to diagnose.
I have tried to visualize in
different visualization tool but still problem was persisting. I was not
able to implement your suggestion regarding tolerance limit of the
visualization software, I used rasmol, chimera, insightII but could not
found any such option. I am still trying for that, if I could found it,
I will inform you the result after that. I am really worried about
temporary LINCE warning
which I was getting. Is there any way to resolve this issue?
I endorse the suggestion Chris made here.
Mark
_______________________________________________
gmx-users mailing list [email protected]
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 [EMAIL PROTECTED]
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
