[gmx-users] Domain decomposition

[Justin Lemkul]

On 7/26/16 2:21 PM, Alexander Alexander wrote:
> On Tue, Jul 26, 2016 at 7:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/26/16 1:16 PM, Alexander Alexander wrote:
>>
>>> On Tue, Jul 26, 2016 at 6:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>>
>>>
>>>>
>>>> On 7/26/16 11:27 AM, Alexander Alexander wrote:
>>>>
>>>> Thanks.
>>>>>
>>>>> Yes indeed it is a free energy calculation in which no problem showed up
>>>>> in
>>>>> the first 6 windows where the harmonic restrains were applying on my
>>>>> amino
>>>>> acid but the DD problem came up immediately in the first windows of the
>>>>> removing charge. Below please find the mdp file.
>>>>> And If I use -ntmpi = 1 then it takes ages to finish. Although my
>>>>> gromcas
>>>>> need to be compiled again with thread-MPI .
>>>>>
>>>>>
>>>>> I suspect you have inconsistent usage of couple-intramol.  Your
>>>> long-distance LJC pairs should be a result of "couple-intramol = no" in
>>>> which you get explicit intramolecular exclusions and pair interactions
>>>> that
>>>> occur at longer distance than normal 1-4 interactions.  If you ran other
>>>> systems without getting any problem, you probably had "couple-intramol =
>>>> yes" in which all nonbonded interactions are treated the same way and the
>>>> bonded topology is the same.
>>>>
>>>>
>>> Actually I always have had "couple-intramol = no" in all my other
>>> calculation(a single amino acid in water solution), and not problem has
>>> shown up. But FEP calculations of the charged amino acid where I have also
>>> an Ion for neutralization of the system and "ion+amino acid" is used as
>>> "couple-moltype", this problem emerges. And if you noticed the Ion here CL
>>> is always one of the atom involving in the problem. I hope
>>> "couple-intramol
>>> = yes"can sove the problem in charged amino acid.
>>>
>>>
>> Well, there are implications for the results.  Consider what it says in
>> the manual.  But yes, this is your problem.  You've got physically separate
>> molecules that you call one [moleculetype] for the purpose of
>> transformation, and you're running into a problem that isn't really
>> physically meaningful in any way.
>>
>
> Actually yes, Ion and amino acid both as  [moleculetype]are really far away
> from each other. But I usually use the final .gro file of the last step as
> input file in the new step, and this separation is what that gro file has.
> I hope " couple-intramol = yes"  can help.
>

Help you in terms of avoiding a DD failure, yes, but you're also completely 
changing the physical picture.  Please read the manual carefully about these 
settings.  You'll probably get distortion if you do this.  Using 
"couple-intramol = no" is more sensible but obviously is causing headaches due 
simply to implementation problems.

>>
>>
>>>> Another question is that if really this amount of pull restrain is
>>>>
>>>>> necessary to be applied on my molecules (singke amino acid) before
>>>>> removing
>>>>> the charge and vdW?
>>>>>
>>>>>
>>>>> You're decoupling a single amino acid?  What purpose do the pull
>>>> restraints even serve?  CA-HA, etc. should be bonded in a single amino
>>>> acid, so why are you applying a pull restraint to them?  I really don't
>>>> understand.
>>>>
>>>>
>>> I want to make sure sudden conformational changes of amino acid do not
>>> occur during the perturbation. In particular, when the charge is turned
>>> off.  Applying a harmonic restraint to keep the geometry the same during
>>> FEP is a well-established procedure, e.g. Deng, Y.; Roux, B. J Chem Theory
>>> Comput 2006, 2 (5), 1255. I might reduce the number of restraints to only
>>> between 1 or 2 pairs.
>>>
>>>
>> Preserving the A-state in the bonded topology (and using couple-intramol =
>> no) will prevent any weirdness from happening without needing any of these
>> restraints.  As in my previous message, restraining CA-HA with a harmonic
>> potential makes no sense at all.  Those atoms have a bond between them.
>> The pull code is not doing anything useful.
>>
>
> Then, If the " couple-intramol = yes" hopefully solves the problem
> discussed above, then, maybe applying restrain in the presence of "
> couple-intramol = yes" is not avoidable.
>
>
>>
>> The whole task is to calculate the binding free energy of amino acid to a
>>> metal surface, although here I am still dealing with the amino acid in
>>> only
>>> water without surface yet.
>>>
>>
>> I believe I've mentioned this before, but in case it got lost along the
>> way - using the free energy decoupling technique is a very ineffective way
>> of calculating this binding free energy.  Do a PMF.  It's extremely
>> straightforward and you don't deal with any of these algorithmic problems.
>> It will also likely converge a lot faster than try to do complex decoupling.
>>
>
> Actually I should have known this in beginning, but, now is a bit late for
> me to switch to PMF.
>

As you like.  You can probably finish a PMF in less than a day for a reasonably 
small system.

-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

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