Also, as far as I understand, before NVE simulation, one should equilibrate the system in the NVT ensemble (at the desired T) and only then switch off T-coupling (=NVE).
Vitaly Chaban >>> 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 -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
