Amit Choubey wrote:
Justin, when i define the whole line charge as a charge group i do get a
coulomb energy contribution. I thought there would be no non-bonded
contribution. I use a very high cut-off (longer than chain length) and
no pbc. Am i missing something ?
Without seeing your .mdp file and the actual energy terms you're observing, I
can only guess. One would think that if it is the only molecule in the system,
there should be no intermolecular Coulombic terms (unless maybe some arise due
to periodicity, but in that case you do not have an infinite system and then
they are artifacts). There may be intramolecular terms (like 1-4) or
PME-related terms.
-Justin
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey <kgp.a...@gmail.com
<mailto:kgp.a...@gmail.com>> wrote:
I was not sure if changing the size of maxcg would not negatively
influence anything else. I will give it a try. Thanks Justin
On Sat, Aug 13, 2011 at 4:04 AM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Amit Choubey wrote:
I change the maximum charge group size defined in the
include/types/nblist.h header from 32 to 267. Then grompp
worked fine but the mdrun did not start. The following error
came out
Program mdrun_jptlc, VERSION 4.5.3
Source code file: ns.c, line: 2417
Fatal error:
Max #atoms in a charge group: 267 > 64
/* Verify whether largest charge group is <= max cg.*
* This is determined by the type of the local exclusion
type *
* Exclusions are stored in bits. (If the type is not large*
* enough, enlarge it, unsigned char -> unsigned short
-> unsigned long)*
*/
The solution is described in the comment above.
maxcg = sizeof(t_excl)*8;
Increase the size here.
-Justin
if (nr_in_cg > maxcg)
{
gmx_fatal(FARGS,"Max #atoms in a charge group: %d >
%d\n",
nr_in_cg,maxcg);
}
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
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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