[gmx-users] User-Specified LJ Epsilon and Sigma
jalemkul at vt.edu
Wed Sep 9 13:32:34 CEST 2015
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.
> On Tuesday, September 8, 2015, Phwey Gil <psg30 at case.edu> wrote:
>> 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
>> 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 Gil
>> Case Western Reserve University | Class of 2016
>> Researcher, Department of Chemical Engineering
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
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jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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