[gmx-users] DrudeFF topology transfer from CHARMM to GROMACS

[Tomasz Piskorz]

Thank you, Justin. That solves my problem.

Best,
Tomasz K. Piskorz



On 31 May 2017 at 13:51, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/31/17 7:06 AM, Tomasz Piskorz wrote:
>
>> Dear all,
>>
>> I would like to simulate cyclohexane using Drude FF in GROMACS. I've seen
>> that the topology is already available in CHARMM-DrudeFF and I would like
>> to transfer it to GROMACS. However, I don't know how to calculate the
>> charge of Drude particle, which is required by topology in GROMACS. Does
>> anyone know how to do it?
>>
>> Atomic polarizability can be described by equation:
>> alpha = (q_D)^2/k,
>> where k = 418400 kJ/(mol*nm^2) and alpha is given in CHARMM topology (i.g.
>> for O in glycine alpha=0.000651 nm^3). However, when I try to calculate
>> the
>> charge I always get a wrong result. Is this question which I should use or
>> there is something more which I don't take under consideration?
>>
>>
> Yes, there is an implicit conversion factor of Coulomb's constant.
>
> qD = sqrt((alpha/kD)/CCELEC)
>
> In CHARMM units, this is
>
> qD = sqrt((0.651/1000)/332.0716)
>
> I'll add the model compounds to the next release of the GROMACS-formatted
> Drude force field.  I have other issues to sort out before doing that,
> though.
>
> -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
>
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