Hi Francesco,
This is not a cuda issue per se but is related to the fact that pmemd itself
does not support the surface area term. You have two options, one would be
to code in the GBSA support basing it on Sander. Volunteers to do this are
welcome. The alternative would be to run your GB MD without the GBSA term
and then post process specific snapshots in Sander to get the GBSA
contribution for that frame. This of course means your dynamics are without
the GBSA term and you are just getting single point energies but this 'may'
be acceptable.
Others might be able to chime in here on how critical it is to have the GBSA
term included in the actual dynamics.
All the best
Ross
> -----Original Message-----
> From: Francesco Oteri [mailto:francesco.oteri.gmail.com]
> Sent: Thursday, March 03, 2011 4:44 AM
> To: amber.ambermd.org
> Subject: [AMBER] implicit solvent with cuda
>
> Dear Amber users,
> I need to use pmemd.cuda with generalized born method but pmemd.cuda
> is
> unable to use a gbsa value greater than 0.
>
> Is it correct to simulate with gbsa=0 because the manual says that with
> gbsa=0 the non polar contribution solvent
> it is excluded from the calculation.
>
> What implicit solvent method i can use to simulate DNA, with pmemd.cuda?
>
>
>
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Received on Thu Mar 03 2011 - 06:30:04 PST
