[gmx-users] User-Specified LJ Epsilon and Sigma

[Justin Lemkul]

On 9/8/15 11:58 AM, Phwey Gil wrote:
> Hi,
>
> I am looking to specify my own parameters for LJ parameters. Using the OPLS
> forcefield, I only want to change the LJ parameters of some atoms.
>
> I have H2O, C8H16O2 (Octanoic acid) and C2H6O (Ethanol).
> I am using SPC/E for H2O, and OPLS for C8H16O2 and C2H6O. And I want to
> change the LJ parameters for the hydrogens in C8H16O2 only.
>
> I have tried specifying [ atomtypes ] in various places (In .top or .itp)
> using the following format:
>
>   [ atomtypes ]
>        H     H      1.008      0.450     A       5.66387665E-4
> 2.80730518E-7
>
> But I was not successful; I checked topol.tpr and the numbers are according
> to OPLS and not my specified values.
>
> Can someone give me advice on how to do this? I've checked the forums and I
> was not successful at finding the correct information.
>

The approach is correct, provided that your topology actually specifies "H" as 
the atom type (note that type and name are totally separate entities).  The new 
[atomtypes] can be added either in ffnonbonded.itp or in the topology directly.

-Justin

-- 
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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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