[gmx-users] Harmonic restraint in FEP

[Justin Lemkul]

On 7/13/16 8:11 PM, Alexander Alexander wrote:
> Perfect explanation, I got it, thanks for that.
>
> As I mentioned, I want to apply this harmonic restraints to avoid
> conformational change in the single amino aicd while perturbation in FEP.
> To do so, the pull restraints comes between pairs of atoms in amino acid,
> each pair contain one reference group and one pull_group as
> [reference_group --pull_group], for example
> [C_alpha--O],[C_alpha--N][C_alpha--H]... [C--H],[C_alpha-C] ...,  this
> makes life a bit hard as multi-referece(if possible) groups as well as
> multi pull-group are required in the pull code.
> So, any other easier suggestion is highly appreciated.
>

You can define any number of restraints you like, and this is the only type of 
restraint that is both useful to you and supported by the free energy code. 
Also consider whether or not such an extensive restraint system is really 
necessary to accomplish what you need.

-Justin

> Thanks.
> Regards,
> Alex
>
> On Wed, Jul 13, 2016 at 11:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/13/16 5:36 PM, Alexander Alexander wrote:
>>
>>> 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.
>>>
>>
>> This is not correct in the general sense.  It depends entirely upon how
>> you define the transformation and/or A-B transitions in the bonded terms.
>> For instance:
>>
>> couple-lambda0 = none
>> couple-lambda1 = vdw-q
>>
>> does the exact *opposite* of what you describe above when moving from
>> lambda = 0 to lambda = 1.  The "direction" of the transformation is up to
>> the user to define.
>>
>> 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 ?
>>>
>>>
>> Similarly, this depends entirely on what you set using pull-coord1-k and
>> pull-coord1-kB.  If you set:
>>
>> pull-coord1-k = 0.0
>> pull-coord1-kB = 1000.0
>>
>> you can turn on the restraint with restraint-lambdas = 0.0 0.2 ... 1.0
>>
>> or you can turn them on with
>>
>> pull-coord1-k = 1000.0
>> pull-coord1-kB = 0.0
>>
>> and restraint-lambdas = 1.0 0.8 ... 0.0
>>
>> Whatever makes the most sense to you.
>>
>>
>> -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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-- 
==================================================

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

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