Our gb model (igb=8) was trained using the Amber resp charge model. I would
expect to have to do careful testing before using with a different charge
set. My guess would be that it would not work well without some adjustment.
I'm not positive but I don't think the CUDA code supports sasa
calculations. Try it and see.
Carlos Simmerling
On Aug 5, 2016 12:06 PM, "Hai Nguyen" <nhai.qn.gmail.com> wrote:
> On Fri, Aug 5, 2016 at 11:54 AM, Chitrak Gupta <chgupta.mix.wvu.edu>
> wrote:
>
> > Hi,
> >
> > I am trying to do an implicit solvent simulation using pmemd.cuda (I am
> > using amber16).
> >
> > One question is, do I need to set a specific surface tension?
>
>
> amber turn off non-polar calculation for implicit solvent simulation as
> default. So you don't need to specify surface tension.
>
>
> > Some MD
> > forums suggest that, but I did not find any reference to this in the
> sample
> > scripts given in the amber16 benchmarking page.
> >
>
> I would suggest to use gbsa=0 (default). Please check previous discussion
> in "[AMBER] gbsa parameter" topic.
>
>
> >
> > Another question is, is the GB solvent model related to the protein
> > parameters? I am asking because I am trying to use CHARMM parameters in
> my
> > simulation. I have done this in the past with explicit solvent
> simulations,
> > but I am not sure if the implicit solvent has to be "consistent" with the
> > force field parameters.
> >
>
> You need to set radii 'bondi', 'mbondi2', 'mbondi3',... to define
> solute/solvent boundary.
> I am not familiar with CHARMM to AMBER topology conversion, so please wait
> for others' feedback.
>
> Hai
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Received on Fri Aug 05 2016 - 10:00:02 PDT
