[gmx-users] zero charge model- simulation time

[Justin A. Lemkul]

Juliette N. wrote:
> 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 ?
> 

Anything that affects the potential will affect the outcome of EM.  Think about 
what you're doing - EM seeks to find the potential energy minimum, which is 
affected by charges according to whatever Coulombic scheme you've employed.

-Justin

> Regards,
> 
> On 28 July 2011 17:44, Justin A. Lemkul <jalemkul at vt.edu 
> <mailto: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> <mailto: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> <http://vt.edu> | (540)
>         231-9080
> 
>            http://www.bevanlab.biochem.____vt.edu/Pages/Personal/justin
>         <http://vt.edu/Pages/Personal/justin>
>            <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 <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

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