[gmx-users] zero charge model- simulation time

[Justin A. Lemkul]

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://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
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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

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