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 - 09:30:03 PDT
