[gmx-users] customized pairtypes with OPLS/AA

[Krzysztof Murzyn]

Justin, Thank you very much. I assume that pairs in pairtypes are used to
calculate 1-4 VdW interactions only and do not influence calculations of
short range VdW?

Regards,
km.

On Wed, Aug 29, 2012 at 6:10 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/29/12 11:37 AM, Krzysztof Murzyn wrote:
>
>> Hi,
>>
>> I want to influence slightly the way VdW interactions are calculated by
>> providing customized values of sigma/epsilon in [ pairtypes ]. I employ
>> OPLS/AA. The section of my molecule definition looks like, say:
>>
>> [ pairtypes ]
>> CT CT 1 0.33 0.2
>>
>>
>> When I run grompp I get the following error message:
>>
>> Program grompp, VERSION 4.5.5
>> Source code file: toppush.c, line: 857
>> Fatal error:
>> Atomtype CT not found
>>
>>
>> What am I doing wrong? Overriding default definition of bondtypes,
>> angletypes, or dihedraltypes works just fine.
>>
>>
> All of those are bonded terms and use atomtype names that are translated
> from their opls_* equivalents.  In ffnonbonded.itp, you need to use opls_*
> atomtypes.
>
> -Justin
>
> --
> ==============================**==========
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> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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