[gmx-users] Harmonic restraint in FEP

[Alexander Alexander]

Thanks Justin for your response.
I have already seen read the manual and every thing is clear for me for the
"coul-lambdas" and "vdW-lambdas"and available examples. As far as I
understand in FEP, when we want to get rid if something gradually for
example vdW or charge, then we go from 0.0 ..... to 1.0 meaning in 0.0 they
are present but in 1.0 they are absent which I think is th same for all the
XXX-lambdas.
So, when I want to turn on or apply or have harmonic restrain then the
restraint-lambdas
should goes from 1.0 to 0.0, however it is in contradict with some examples
in which the harmonic restraint is going to be applied and that confuse me
a bit.

In summary, I want to apply gradually harmonic restraints, so,
reasonably, restraint-lambdas
= 1.0 0.8 0.6 0.4 ... 0.0 ?

Thanks,
Regards
Alex



On Wed, Jul 13, 2016 at 10:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/13/16 3:52 PM, Alexander Alexander wrote:
>
>> Dear Gromacs user,
>>
>> To avoid conformational changes of a single amino acid while it is
>> perturbed (vdW and q --> 0) in Free energy calculation, I need to apply a
>> harmonic restraints on(or between?) some of it's atoms by [
>> distance_restraints ] and "restraint-lambdas".
>>
>> First of all, is this right? I means " "restraint-lambdas" can be used
>> for [
>> distance_restraints ]?
>>
>>
> No.  You can only modulate dihedral restraints and the pull code (which is
> what you should be using anyway):
>
>
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#free-energy-calculations
>
> If so, how can I find out proper "low, up1, up2 and fac" for a molecule?
>>
>> One more question is that what the "restraint-lambdas" should be look like
>> when harmonic restraints is going to be applied(turning on gradually) by
>> whatever method?
>>
>>
>> restraint-lambdas   = 1.0 0.8 0.6 0.4 0.2 0.0
>> OR
>> restraint-lambdas   = 0.0 0.2 0.4 0.6 0.8 1.0
>>
>>
> See available options in
> http://manual.gromacs.org/documentation/5.1.2/user-guide/mdp-options.html#com-pulling
>
> The A-state is 0 and the B-state is 1.  The behavior of restraint-lambdas
> depends on how you choose/need to set up the restraints themselves.
>
> -Justin
>
> --
> ==================================================
>
> 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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