[gmx-users] how to simulate a line charge

[Justin A. Lemkul]

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.amit at gmail.com 
> <mailto:kgp.amit at 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 <jalemkul at vt.edu
>     <mailto:jalemkul at 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>
> 
>         ==============================__==========
>         -- 
>         gmx-users mailing list    gmx-users at gromacs.org
>         <mailto:gmx-users at gromacs.org>
>         http://lists.gromacs.org/__mailman/listinfo/gmx-users
>         <http://lists.gromacs.org/mailman/listinfo/gmx-users>
>         Please search the archive at
>         http://www.gromacs.org/__Support/Mailing_Lists/Search
>         <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 gmx-users-request at gromacs.org
>         <mailto:gmx-users-request at gromacs.org>.
>         Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>         <http://www.gromacs.org/Support/Mailing_Lists>
> 
> 
> 

-- 
========================================

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

========================================