Re: GBIS CUDA not yet compatible with fixed atoms

From: Siva Dasetty (
Date: Fri Sep 05 2014 - 15:24:45 CDT

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


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

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