Re: GBIS CUDA not yet compatible with fixed atoms

From: Aron Broom (
Date: Fri Sep 05 2014 - 16:50:39 CDT

I don't think you can turn it off for one particular portion of the system.

Keep in mind also, that while it may not be charged, and hence the GBIS
portion may not be needed, if you do not have solvent, you may still want
the SASA component for the correct hydrophobic effect (which, by contrast
to GBIS, would probably be very important for your graphene surface).
 Though it's been pointed out to me that implicit solvent calculations, by
virtue of not having water molecules creating interactions, actually
already reproduce a significant portion of the hydrophobic effect without
the need for the SASA correction (which I believe you can turn off
separately from running GBIS).

On Fri, Sep 5, 2014 at 4:24 PM, Siva Dasetty <> wrote:

> Thank you for the reply. I forgot to add, but this note actually made me
> realize that I don't need to do GBIS/SASA calculations for my graphene
> surface as 1. it is not charged and 2. it is unnecessary.
> So Is there any way that I can exclude GBIS for a particular group in
> NAMD? In this case, exclude GBIS calculation for graphene and include for
> the protein.
> Thanks,
> Siva
> On Fri, Sep 5, 2014 at 4:16 PM, Jim Phillips <> wrote:
>> This message only applies to the GBIS implicit solvent code. The NAMD
>> CUDA code for explicit solvent does support fixed atoms.
>> I don't understand why this is and error. At the very least GBIS should
>> be compatible with fixed atoms if fixedAtomsForces is set. I've revised
>> the error test to automatically enable fixedAtomsForces and this should be
>> available in the next nightly build. Please test tomorrow.
>> Jim
>> On Fri, 5 Sep 2014, Siva Dasetty wrote:
>> Dear All,
>>> I am running a test simulation to check the performance of GBIS with
>>> CUDA.
>>> My system involves graphene which is fixed and protein in implicit
>>> solvent.
>>> However when I try to run I get the following error " GBIS CUDA not yet
>>> compatible with fixed atoms".
>>> Does that mean, NAMD cuda doesnt support fixed atoms yet or am I doing
>>> something wrong?
>>> Thanks,
>>> Siva
> --
> Siva Dasetty
> PhD Student
> Department of Chemical and Biomolecular Engineering
> Clemson University
> Clemson, SC 29634

Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo

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