[gmx-users] scaling non-bonded interactions

[Justin A. Lemkul]

Kukol, Andreas wrote:
> FudgeLJ does only work when the pairs are generated automatically. If they are specified explicitly as in the Gromos forcefields, FudgeLJ has no effect.
> 

I see two ways to get around this problem:

1. Specify pairs manually (which may be tedious)
2. Minimize with a force field that does generate pairs with reduced FudgeLJ and 
FudgeQQ values, then re-minimize with Gromos, which I take it is the desired 
force field.

-Justin

> Andreas
> ________________________________________
> From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of Justin A. Lemkul [jalemkul at vt.edu]
> Sent: 01 June 2011 20:38
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] scaling non-bonded interactions
> 
> Da-Wei Li wrote:
>> I remember that 1-4 won't be scaled in the free energy code, right?
>>
> 
> True, but the desired 10% scaling in this case can be applied by changing the
> FudgeLJ and FudgeQQ values of the force field, I believe.
> 
> -Justin
> 
>> dawei
>>
>> On Wed, Jun 1, 2011 at 3:24 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>>     Kukol, Andreas wrote:
>>
>>         Hello,
>>         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.
>>
>>
>>     You can do this with the free energy code.
>>
>>     couple-moltype = system
>>     init_lambda = 0.9
>>     couple_lambda0 = vdw-q
>>     couple_lambda1 = none
>>
>>     Please note, though, that such settings will result in massive
>>     performance loss, even for small systems.  There is an open issue on
>>     the redmine server about this, but no resolution yet.
>>
>>     -Justin
>>
>>     --
>>     ========================================
>>
>>     Justin A. Lemkul
>>     Ph.D. Candidate
>>     ICTAS Doctoral Scholar
>>     MILES-IGERT Trainee
>>     Department of Biochemistry
>>     Virginia Tech
>>     Blacksburg, VA
>>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>>     <tel:%28540%29%20231-9080>
>>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>     ========================================
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> 
> --
> ========================================
> 
> 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
> 
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-- 
========================================

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

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