[gmx-users] CHARMM36 ff with NBFIX in grimaces

[gozde ergin]

Thanks Justin.

In order to validate the results from Luo and Roux 2010 study, I need to run the simulations with and without NBFIX.
But thank you very much for your respond, I appreciate it.


> On 12 Apr 2016, at 13:25, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> 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 <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul <http://mackerell.umaryland.edu/~jalemkul>
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists <http://www.gromacs.org/Support/Mailing_Lists>
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send a mail to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.