[gmx-users] using OH ions in combination with CHARMM27 force field

[Justin Lemkul]

On 12/10/15 8:57 AM, soumadwip ghosh wrote:
> Hi all,
>           I am trying to simulate a polymer membrane in the presence of
> electrolytes. As an effort to corroborate experimental outcomes I have to
> do simulation in the presence of 0.1M NaOH. I know that OH- is present in
> the standard CHARMM FF directory. So, I tried to add 15 Na (+) and 15 OH(-)
> in the system which happened without any error. Now, while executing grompp
> for energy minimization I got this strange error of the no. of coordinates
> in the gro file does not match that of the .top file and the difference is
> 15 less in the .gro file. Now the thing is I can see that genion has added
> the required no. of OH(-) in the system and the topology file has been
> updated accordingly. However, if I add CL instead of the hydoxide ion
> things go smoothly and grompp does not scream. Is there something anyone
> knows about this kind of weird behavior of the ions? I am using GROMACS
> 5.0.5. Any sort of help will be appreciated. Following are my files-
>

genion does not add polyatomic ions, so without seeing exactly what you did and 
what your topology and coordinates look like, all I can say is that probably 
something went wrong there (a difference of 15 atoms is a strong clue).  To add 
polyatomic species, use genbox/insert-molecules -ci -nmol, not genion.

-Justin

> topol.top
>
> ; Include the force field
> #include "charmm27.ff/forcefield.itp"
>
> ;Include CHARMM atomtypes
> #include "atomtypes_nafion.itp"
>
> ; Include chain topologies
> #include "nafion.itp"
>
> ; Include water topology
> #include "charmm27.ff/tip3p.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>     1    1       1000       1000       1000
> #endif
>
> ; Include generic ion topology
> #include "charmm27.ff/ions.itp"
>
> [ system ]
> nafion and ions in water
>
> [ molecules ]
> LIG             1
> SOL            7997
> NA              15
> OH              15
>
> Regards,
> Soumadwip Ghosh
> Research Scholar
> IITB
> India
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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