[gmx-users] problem using pairtypes 2, 3 for free-energy decoupling

[Alexey Shaytan]

Dear David, all,

I'm not 100% sure that i'm doing everything right, mainly because I have
found only a slight record about pairtypes 2,3 in the manual.
And on the revision list for GROMACS 3.3 this feature is the very last on
the list. So I wonder if it was really implemented in 3.3.1 release?

However, it seems to me that grompp (3.3.1) really disregards the
interaction type for pairs. E.g. setting arbitary function type (like 8 or
9) for pair interactions gives no error message whereas doing the same for
other forcefiels directives would yield an error: interaction type
undefined.

Thanks,
Alexey

> Alexey,
>
>
> I notice you haven't received a response on this; if you are convinced
> you're doing the right thing, you might try submitting a bugzilla so the
> developers can reproduce your problem.
>
> Thanks,
> David
>
>
>
> On 7/31/06, Alexey Shaytan <shaytan at polly.phys.msu.ru> wrote:
>
>> Dear Michael, Berk, all
>>
>>
>> I'm currently trying to use GROMACS for calculation of solvation free
>> energies for small molecules in water and hexane.
>>
>> Searching through the mailing archives I found the following method
>> to decouple solvent-solute interactions:
>>
>> Berk Hess Wed Mar 1 09:30:25 CET 2006 wrote:
>>
>>
>>> The idea is that for the solute to be decoupled one would replace
>>> the in its [ pairs ] section type 1 by type 2 and exclude all
>>> intramolecular non-bonded interactions and replace add them again
>>> explicitly in a [ pairs ] section as type 3.
>>>
>>
>> However, trying to realize this method in GROMACS 3.3.1 release I
>> encountered a problem: it seems that in my case grompp or mdrun
>> disregards the type of pair interaction, assuming it always to be 1. And
>> the pair interactions ARE pertubed during the free energy calculation.
>>
>> So setting the pairs topology parameters as
>> --------------------
>> [ pairs ]
>> ; ai aj funct
>> 2  5  1
>> ........
>> --------------------
>> or ----------------------
>> [ pairs ]
>> ; ai aj funct
>> 2  5  2
>> ..........
>> ---------------------
>> yields the same results, when the free energy lambda is set to 1
>> (topology
>> B). In my case the pair interactions are switched off, that is
>> undesirable.
>>
>> Can anybody help me to figure out what the problem can be?
>>
>>
>>
>> Thanx in advance,
>> Alexey
>>
>>
>> --
>> Alexey Shaytan
>> Chair of Polymer and Crystal Physics
>> Faculty of Physics
>> Moscow State Lomonosov University
>> Tel: +79037411176
>> e-mail: shaytan at polly.phys.msu.ru
>> Web: http://polly.phys.msu.ru/~shaytan/
>>
>>
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>


-- 
Alexey Shaytan
Chair of Polymer and Crystal Physics
Faculty of Physics
Moscow State Lomonosov University
Tel: +79037411176
e-mail: shaytan at polly.phys.msu.ru
Web: http://polly.phys.msu.ru/~shaytan/