[gmx-developers] calculating poteintial energy into do_md()

[Shirts, Michael (mrs5pt)]

> Actually I did it but I the performance decrease a lot (2x).
> In particular I run the same run with free_energy  = yes and free_energy =
> no and in the second case the run is 2times faster.
> I found in the mailing list that this performance drop is known.

What are the particular parameters you are trying to change?  I wrote the
new Hamiltonian Exchange code, so I'm interested in making sure it's as
useful as possible.  There might be some cases where this performance drop
can be avoided, and   It's likely the PME parameters, since doing repeated
that's the only thing that really makes free energy slow.

UNLESS of course you are changing ALL of the atoms, which which case all of
them will go through the free energy code, and it certainly will be slower.
There are some possible ways to fix this, but that will not be until 5.0.
 
Best,
~~~~~~~~~~~~
Michael Shirts
Assistant Professor
Department of Chemical Engineering
University of Virginia
michael.shirts at virginia.edu
(434)-243-1821


> From: francesco oteri <francesco.oteri at gmail.com>
> Reply-To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Date: Mon, 16 Jul 2012 14:08:49 +0200
> To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
> Subject: Re: [gmx-developers] calculating poteintial energy into do_md()
> 
> Dear Berk
> 
> 2012/7/16 Berk Hess <hess at kth.se>
> 
>>  On 7/16/12 13:05 , francesco oteri wrote:
>> 
>>  Dear gromacs developers,
>> I am trying to implement in gromacs 4.5.5 a particular Hemiltonian Replica
>> Exchange tecnique.
>> Right now, at every exchange attempt in do_md, I figured out  how to
>> access at the potential
>> energy of replica A (=configuration A at temperature A) and B
>> (=configuration B at temperature B) and so on.
>> 
>> In my case, each replica has the same temperature, but there is a
>> different Hemiltonian equation for every replica.
>> The different Hemiltonian are obtained simply changing the force field
>> parameters in the input topology so I dont
>> need to modify anything in gromacs.
>> 
>>  But at every exchange attempt I have to test if the configuration B can
>> exist in the state A so I need to calculate
>> its potential energy using the force field data of replica A.
>> 
>>  I found that function sum_epot calculates the potential energy but I
>> suspect that it uses values calculated in
>> do_force since sum_epot is called by do_force_lowlevel in turn called by
>> do_force.
>> 
>> 
>> 
>>  So my question is, should I call do_force in replica A with coordinates
>> from replica B reach my goal?
>> 
>> Yes.
>> Are you changing bonded and/or non-bonded parameters?
>> Some non-bonded parameters might be preprocessed, so you might need
>> reprocess those
>> and them reprocesses again to get back to the original state.
>> 
>> 
> Which parameters need such a preprocessing?
> 
> 
> 
>> Note that 4.6 will have proper Hamiltonian replica exchange, but that will
>> use the lambda coupling
>> parameter approach. If you need to do something similar, it might be much
>> simpler to use this code.
>> 
>> 
> 
> Actually I did it but I the performance decrease a lot (2x).
> In particular I run the same run with free_energy  = yes and free_energy =
> no and in the second case the run is 2times faster.
> I found in the mailing list that this performance drop is known.
> 
> Since I dont need to change lambda along the simulation, I prefer using a
> modified input topology and running a normal REMD changing something in
> repl_ex.c and md.c.
> 
> Of course, any suggestions to improve performance are wellcome :)
> 
> 
> 
> 
> Cheers,
>> 
>> Berk
>> 
>> 
>>  Thanks in advance,
>> 
>>  Francesco
>> 
>> 
>> 
>> 
>> 
>> 
>> --
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> 
> 
> 
> -- 
> Cordiali saluti, Dr.Oteri Francesco
> -- 
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