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

[Maryam Kowsar]

Hi justin
Actually i modified the forcefield parameters to introduce atoms that are
not present in that. I think you are right in the case that we want to
change bonded or nonbonded parameters in the forcefield

On Wednesday, September 9, 2015, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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:;>
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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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