[gmx-users] Re: Secondary structure loss in implicit solvent simulations

Michael Shirts mrshirts at gmail.com
Tue Jan 25 18:48:28 CET 2011

OK, that is what I was trying to figure out -- is the problem
reproducible on both GPU and CPU.  Now, you havent answered the direct
question, if the energies are the same for at least the first 5 steps
are so -- without that knowledge, then here might be different errors
occurring in GPU vs CPU.

At this point, the question is then whether this works with another
code with the same input parameters.  Sander (part of the AmberTools
system)is downloadable (I believe to anyone, not just academics), so
you can try running the same system on Sander, using the best fit to
the implicit solvent model in gromacs.

If THAT works, and Gromacs GPU fails, then it would appear to be a
problem with Gromacs implicit solvent implementation, and should be
posted to redmine as a bug, as well as described on the list with full
details (more than you have provided so far!) so that it can be
reproduced by the developers.


On Tue, Jan 25, 2011 at 5:05 AM, K. Singhal <k.singhal at uva.nl> wrote:
> Hi
> It's not necessarily GPU-specific, it's implicit solvent-specific. I don't get these problems in explicit solvent simulations on CPU, only in implicit solvent simulations both on GPU as well as CPU. One of the problems that I can think of is unbalanced charges that I would have balanced out using NaCl ions, but not any more.
> Regards
> Kush
> --
> Kushagra Singhal
> Promovendus, Computational Chemistry
> van 't Hoff Institute of Molecular Sciences
> Science Park 904, room C2.119
> 1098 XH Amsterdam, The Netherlands
> +31 205256965
> Universiteit van Amsterdam
> k.singhal at uva.nl
> --
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