[gmx-users] Re: scaling non-bonded interactions

[Kukol, Andreas]

I want to use it to energy minimise a system that has severe clashes. The EM always crashes, even if I reduce the step-size. It could also be useful for NMR refinement to allow atoms to move through each other in order to satisfy distance restraints.

Andreas
________________________________________
From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Vitaly Chaban [vvchaban at gmail.com]
Sent: 01 June 2011 20:30
To: jalemkul at vt.edu
Cc: gmx-users at gromacs.org
Subject: Re: [gmx-users] Re: scaling non-bonded interactions

Doesn't increased temperature work for this purpose?



On Wed, Jun 1, 2011 at 3:27 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Vitaly Chaban wrote:
>>>
>>> Is it possible to globally scale all non-bonded interactions by a factor
>>> ?  I know there are energy exclusion groups, but that is an all or nothing
>>> approach, while I would like to reduce non-bonded interaction potentials to
>>> e.g. 10% of their normal value.
>>>
>>> If this is not possible, I suggest to have this as an option in the
>>> mdp-file.
>>
>>
>> I don't see much sense in such uniform scaling.
>>
>>
>
> Such scaling can be useful for overcoming energy barriers and speeding up
> equilibration.  This function is hinted at in the description of the
> couple-moltype .mdp keyword.  I don't know if that's the intent here, but it
> certainly does have an application.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>



--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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