[gmx-users] how to simulate a line charge
kgp.amit at gmail.com
Sun Aug 14 19:44:12 CEST 2011
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 ?
On Sat, Aug 13, 2011 at 3:21 PM, Amit Choubey <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> 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
>> The solution is described in the comment above.
>> maxcg = sizeof(t_excl)*8;
>> Increase the size here.
>> if (nr_in_cg > maxcg)
>>> gmx_fatal(FARGS,"Max #atoms in a charge group: %d > %d\n",
>> 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
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