Hi Thomas,
thanks again for helping me to understand !
Of course that now the "trick" with two sander jobs is clear,
so I didn.t mention it in my last email.
Thanks also for pointing to two key source files but I think
that for the moment I will survive with the actual level of understanding
:))
Let.s just hope that this elegant technique will be soon implemented also
in pmemd.cuda.
Best wishes,
Marek
Dne Fri, 09 Dec 2011 21:27:24 +0100 <steinbrt.rci.rutgers.edu> napsal/-a:
> Hi Marek,
>
>> My actual interpretation of the implementation of general formula
>>
>> V(L) = (1-L) V0 + L V1
>>
>> is that during the MD run with the given L value in the given time step
>> ti
>>
>> a) the atom interactions (potentials, forces) are calculated according
>> to
>> potential V0, using the actual coordinates
>> b) the atom interactions (potentials, forces) are calculated according
>> to
>> potential V1, using the actual coordinates
>
> but a and b are done on different processors, so its not slower than a
> non-TI run.
>
>> c) the final atom interactions (potential energy, final forces necessary
>> to propagate the system in time) are calculated
>> as the L-linear combination of those calculated in a) and b).
>>
>> Then also dV/dL is calculated (here simple as V1-V0).
>
> that is exactly what thermo_inf.f does, plus mix the forces as well to
> propagate with the mixed potential. The only additional complication is
> that if softcore atoms exist, parts of the potential are no longer linear
> in lambda. All the additional derivative and energy components for that
> case are collected at many different points in the code, so this is a bit
> more tricky to go through (module softcore.f provides a good start).
>
>> I thing that for all technical details the best way is really to check
>> relevant source files.
>
> That is technically true, but I know that sander code (and any other
> program written by someone else) is hard to read, especially the
> optimized
> and parallel parts. Nevertheless, sometimes only the source can tell you
> whats really going on :-)
>
> Kind Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Sat Dec 10 2011 - 09:30:02 PST
