Adwait Mevada wrote:
<snip>
I would not say that you tube rotates so vigorously to be
suspicious... The tube is also very small. What about trying a bigger
one, e.g. with about 1 000 atoms? It should be more inert, if you'd
like it to be such.
ok. I will do that and tell you what happens.
hope this might be useful:
they are top and sideviews
http://www.youtube.com/watch?v=aMMa4o0CzxU
http://www.youtube.com/watch?v=UVksVaHcw8U
http://www.youtube.com/watch?v=xJu3NSkA3gU
http://www.youtube.com/watch?v=cdcyqnPY7D4
So, now the problem becomes why NVE simulation does not preserve
system energy. I did not find above what method you used (MDP file)
for the LJ interactions. I believe the problem is someplace around
this point.
I do not get you, surely the itp & top files will have the information
regarding
the LJ interactions. As far as i remember for C-C interactions I have C6
and C12 interaction mentioned in [non_bond param] section and also when
defining the atom type C I have used the same parameter values, is there
anything else i have to take into consideration besides that?
-Adwait
You didn't set "vdwtype" in your .mdp file, but in this case it should default
to "cutoff," which I don't think is a problem. What might be an issue is your
treatment of PBC. If your box is somewhat small, your system will experience
repulsion from forces derived from periodic copies of your molecule. The proper
approach for a vacuum simulation would be to set "pbc = no" and set all cutoffs
to 0 to capture all intramolecular interactions.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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