[gmx-users] how to simulate a line charge

[Amit Choubey]

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
>>> 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 | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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