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

[Justin Lemkul]

On 9/9/15 7:29 AM, Maryam Kowsar wrote:
> Hi dan
> I think that's not possible to change forcefield parameters and use the old
> defined forcefield like opls. When you change the parameters in .itp you
> should introduce your own forcefield. Try to have all the needed files of
> forcefield in a new folder and use that during making topology.
>

This is not true. Any force field can be modified or extended. A local copy of a 
modified force field is a safe recommendation, but in the case of simply adding 
new atom types, there's little harm that can be done.

-Justin

> On Tuesday, September 8, 2015, Phwey Gil <psg30 at case.edu> 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.
>>
>> Best Regards,
>>
>> Dan
>>
>> --
>> Dan Gil
>> Case Western Reserve University | Class of 2016
>> Researcher, Department of Chemical Engineering
>> psg30 at case.edu <javascript:;>
>> --
>> Gromacs Users mailing list
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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

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