On 7/6/12 3:56 PM, James Starlight wrote:
Justin,
I've experimented with 2 dirrerent COM groups
comm-grps = SOL_NA_CL XW Protein_CCl4_ADN ; 3 groups
comm-grps = SOL_NA_CL_XW Protein_CCl4_ADN; 2 groups
but the crashes were in both cases after 12- 15ns of simulation
this time I've changed to the
comm-grps = System
and there have not been any crashes yet (to this time I've already
calculated addition 20ns after privious crhased simulation using
checkpoint file for the last simulation ). But it's posible that it
was lucky coincidence :)
Could you tell me how I could devide largest group in the above
axample into several smaller sub-groups ? Should I do that separation
randomly or there are most correct way for that ? (e.g within third
cgnr separate all nitrogens and oxygens with corresponded hydrogens in
the separate cgrp's from carbons)
Look at existing examples in the force field .rtp file. In general, a charge
group consists of a functional group (amine, carboxylate, etc) or small CHn
units. Generally there are 2-4 atoms per charge group. There is some
discussion on these topics in the manual.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list [email protected]
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Only plain text messages are allowed!
* 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
