[gmx-users] Conversion between nonbonded charmm NBFIX and gromacs cross terms

[Marlon Sidore]

Thanks for your answer, that solved everything.

Marlon

Marlon Sidore


PhD Student
Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
CNRS - UMR7255
31, Chemin Joseph Aiguier
13402 cedex 20 Marseille
France


2016-07-21 14:01 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 7/21/16 5:01 AM, Marlon Sidore wrote:
>
>> Hello,
>>
>> I am currently translating non-bonded parameters from CHARMM to GROMACS,
>> which include/necessitate cross terms for the forcefield I'm interested in
>> (MARTINI).
>>
>> I am struggling at the conversion from the NBFIX lines, which have this
>> shape:
>> "P5 P5 -1.33843000 5.27557163
>> P5 Nda -1.19503000 5.27557163"
>>
>
> So you're not dealing with CHARMM, but you're dealing with MARTINI
> parameters that happen to be in CHARMM format, correct?
>
> To something gromacs like, which have this shape:
>> "  P5    P5  1   0.24145E-00     0.26027E-02 ; supra attractive
>>   P5    Nda     1   0.21558E-00     0.23238E-02 ; attractive"
>>
>> I think I understood that CHARMM uses Rmin and Emin(epsilon) and GROMACS
>> uses c6 and c12. But I'm currently stuck at how to translate the former
>>
>
> Force fields use whichever convention is specified in the [defaults]
> directive. The combination rule there can either specify the use of
> sigma/epsilon or C6/C12 conventions.
>
> CHARMM files specify epsilon and Rmin directly, so the conversions should
> be straigtforward:
>
> epsilon (GMX) = epsilon (CHARMM) * 4.184 (and given as a positive value,
> by convention)
>
> sigma (GMX) = Rmin (CHARMM) * 2^(-1/6) / 10
>
> The values you have listed above have gone through the additional
> transformation of being converted to C6/C12 (after being converted to
> sigma/epsilon) by equation 5.1 in the manual for combination rule 1.
>
> -Justin
>
> into the latter, as it doesn't seem like a simple scaling - since in this
>> example 2 numbers from CHARMM are the same while none are the same in
>> GROMACS.
>>
>> Thanks for your help
>>
>> Marlon Sidore
>>
>>
>> PhD Student
>> Laboratoire d'Ingénierie des Systèmes Macromoléculaire (LISM)
>> CNRS - UMR7255
>> 31, Chemin Joseph Aiguier
>> 13402 cedex 20 Marseille
>> France
>>
>>
> --
> ==================================================
>
> 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
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.