[gmx-users] zero charge model- simulation time

[Juliette N.]

Hello Justin,

I am using tpbconv to set zero charges after em and after doing grompp_md.

grompp -f *.mdp -c *_em.gro -p *.top -o *_md.tpr

tpbconv –s *_md.tpr -o *-ZERO_md.tpr –zeroq

mdrun -s *-ZERO_md -o -c  -e -x -v
Do I need to use tpbconv after grompp_em? (before mdrun_em)

Regards,

On 28 July 2011 14:53, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Juliette N. wrote:
>
>> Hi again,
>>
>> I am wondering if using tpbconv to set zero charges (case 1) works similar
>> to when one sets zero atom charges in topology file from the very beginning
>> (case 2). Do these two cases work similarly?
>>
>>
> They should work identically.
>
>
>  I checked tpr file and I see that charges are set to zero.
>>
>> Can you please tell me what these lines mean?
>>
>> Does it refer to exclusion which is set to 3 in top file?
>>
>>
> Yes.
>
>
>  excls[0][0..10]={0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10}
>>         excls[1][11..18]={0, 1, 2, 3, 4, 5, 6, 7}
>>
>> The number of these lines corresponds to atom numbers in the system.
>>
>>
> They refer to the atom indices of the atoms in the [moleculetype], not the
> consecutive numbering of the system (for the first molecule this will be the
> same, but I thought I'd point that out).
>
>
> -Justin
>
> --
> ==============================**==========
>
> 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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-- 
Thanks,
J. N.
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