[gmx-users] zero charge model- simulation time

[Juliette N.]

sorry Justin to get back to you gain. This means I have to set zero charges
twice ( after grompp EM and grommp MD), since in grompp_md I am using
topology file which sets actual charges again to all atoms. Do atoms charges
affect EM configuration ?

Regards,

On 28 July 2011 17:44, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Juliette N. wrote:
>
>> 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)
>>
>>
> If you want to do energy minimization with zero charges, then yes.
>
> -Justin
>
>  Regards,
>>
>>
>> On 28 July 2011 14:53, Justin A. Lemkul <jalemkul at vt.edu <mailto:
>> 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 <http://vt.edu> | (540) 231-9080
>>
>>    http://www.bevanlab.biochem.__**vt.edu/Pages/Personal/justin<http://vt.edu/Pages/Personal/justin>
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>> >
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>> --
>> Thanks,
>> J. 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
> 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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