Ok. I agree with you, FEP performance is an important issue to resolve but I
know that there are also other priorities. However, I would thank you for your
interest and and your suggestions.
Luca
> I would suggest that you take Chris' advice and post all of this as a
> feature request on redmi
I would suggest that you take Chris' advice and post all of this as a feature
request on redmine.gromacs.org so that it can be put on a to-do list. Enhancing
the performance of the free energy code is probably going to be a low-priority,
long-term goal (in the absence of any proven bug), but
I posted my test files in:
https://www.dropbox.com/link/17.-sUcJyMeEL?k=0f3b6fa098389405e7e15c886dcc83c1
This is a run for a dialanine peptide in a water box.
The cell side cubic box was 40 A.
The directory is organized as :
TEST\
topol.top
Run-00/confout.gro; Equilibrated stru
David Mobley wrote:
Hi,
This doesn't sound like normal behavior. In fact, this is not what I
typically observe. While there may be a small performance difference,
it is probably at the level of a few percent. Certainly not a factor
of more than 10.
I see about a 50% reduction in speed when
Hi,
This doesn't sound like normal behavior. In fact, this is not what I
typically observe. While there may be a small performance difference,
it is probably at the level of a few percent. Certainly not a factor
of more than 10.
You may want to provide an mdp file and topology, etc. so someone ca
I followed your suggestions and i tried to perform a MD run wit GROMACS and
NAMD for dialanine peptide in a water box. The cell side cubic box was 40 A.
GROMACS:
With the free energy module there is a drop in gromacs performance of about
10/20 fold.
Standard MD: Time: 6.693 6
Yes i am testing the possibility to perform an Hamiltonian-REMD
Energy barriers can be overcome increasing the temperature system or scaling
potential energy with a lambda value, these methods are "equivalent".
Both have advantages and disavantages, at this stage it is not the right place
to de
Chris Neale wrote:
>> Dear Chris and Justin
/ Thank you for your precious suggestions
/>>/ This is a test that i perform in a single machine with 8 cores
/>>/ and gromacs 4.5.4.
/>>/
/>>/ I am trying to enhance the sampling of a protein using the decoupling scheme
/>>/ of the free ener
Luca Bellucci wrote:
Dear Chris and Justin
Thank you for your precious suggestions
This is a test that i perform in a single machine with 8 cores
and gromacs 4.5.4.
I am trying to enhance the sampling of a protein using the decoupling scheme
of the free energy module of gromacs. However
Dear Chris and Justin
Thank you for your precious suggestions
This is a test that i perform in a single machine with 8 cores
and gromacs 4.5.4.
I am trying to enhance the sampling of a protein using the decoupling scheme
of the free energy module of gromacs. However when i decouple only the
Luca Bellucci wrote:
Hi Chris,
thank for the suggestions,
in the previous mail there is a mistake because
couple-moltype = SOL (for solvent) and not "Protein_chaim_P".
Now the problem of the load balance seems reasonable, because
the water box is large ~9.0 nm.
Now your outcome makes a lo
Hi Chris,
thank for the suggestions,
in the previous mail there is a mistake because
couple-moltype = SOL (for solvent) and not "Protein_chaim_P".
Now the problem of the load balance seems reasonable, because
the water box is large ~9.0 nm.
However the problem exist and the performance loss is v
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