[gmx-users] CHARMM36 ff with NBFIX in grimaces

[Justin Lemkul]

On 4/12/16 5:35 AM, gozde ergin wrote:
> Dear all,
>
> I try to simulate the salt solution by using charmm36 ff in gromacs.
> I downloaded charmm36.ff from MacKerell web page.
>
>
> forcefield.to file ;
>
> ; This force field generated by charmm2gmx.py from
> ; multiple charmm parameter files
> ; and multiple charmm topology files
> #define _FF_CHARMM
>
> ; This gromacs version created from:
> ; CHARMM parameters: multiple files
> ; CHARMM topology: multiple files
> [ defaults ]
> ; nbfunc	comb-rule	gen-pairs	fudgeLJ	fudgeQQ
> 1	2	yes	1.0	1.0
>
> #include "ffnonbonded.itp"
> #include "ffbonded.itp"
> #include "gb.itp"
> #include "cmap.itp"
> #include “nbfix.itp"
>
> So the last line is nbfix.itp so I assume this force filed comes with non-bonded fix parameter.
> But if I want to simulate without NBFIX parameter should I remove this line?
>

You can, but I don't know why you'd want to.  The NBFIXes are considered 
integral parts of the force field.  If you take them out, you'll risk spurious 
ion pairing, incorrect osmotic pressure and diffusion, etc. not to mention 
incorrect interactions among some biomolecules.

-Justin

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

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

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