From: David Minh (daveminh_at_gmail.com)
Date: Wed Dec 05 2012 - 09:56:09 CST
Short of modifying the NAMD code, I think it is the only way. I've had to
do this too.
On Wed, Dec 5, 2012 at 7:52 AM, jesmin jahan <shraban03_at_gmail.com> wrote:
> Dear NAMD users,
>
> I am new to NAMD.
>
> I am comparing performance of several MD packages (for example Amber,
> Gromacs &NAMD) wrt to the computation of GB energy. For this, I need
> to know the GB energy value along with the time to compute the
> GB-energy value for NAMD.
>
> I wanted to know whether there is a way to compute the GB energy
> without calculating any other kind of energy terms.
>
> By this I mean to turn off all bonded energy and VWD energy terms.
> Also, I do not want to compute the GB forces, I only want the energy
> value.
>
> So far, what I have done is to run single point simulation by first
> turning the GBIS off and then GBIS on. Then I am taking the difference
> in the Electrostatic energy value from these two simulations to get
> the GB energy value.
>
> To get the running time, I am taking the difference of GBIS on-GBIS off
> run.
>
> Now, my question is, Is there any better way to do this?
>
> If anyone can help me with this, that will be really appreciable.
>
> Thanks in advance,
> Jesmin
>
> On Mon, Dec 3, 2012 at 9:34 PM, jesmin jahan <shraban03_at_gmail.com> wrote:
> > Dear NAMD users,
> >
> > I am new to NAMD.
> >
> > I am comparing performance of several MD packages (for example Amber,
> > Gromacs &NAMD) wrt to the computation of GB energy. For this, I need
> > to know the GB energy value along with the time to compute the
> > GB-energy value for NAMD.
> >
> > I wanted to know whether there is a way to compute the GB energy
> > without calculating any other kind of energy terms.
> >
> > By this I mean to turn off all bonded energy and VWD energy terms.
> > Also, I do not want to compute the GB forces, I only want the energy
> > value.
> >
> > So far, what I have done is to run single point simulation by first
> > turning the GBIS off and then GBIS on. Then I am taking the difference
> > in the Electrostatic energy value from these two simulations to get
> > the GB energy value.
> >
> > To get the running time, I am taking the difference of GBIS on-GBIS off
> run.
> >
> > Now, my question is, Is there any better way to do this?
> >
> > If anyone can help me with this, that will be really appreciable.
> >
> > Thanks in advance,
> > Jesmin
> >
> > --
> > Jesmin Jahan Tithi
> > PhD Student, CS
> > Stony Brook University, NY-11790.
> >
>
>
>
> --
> Jesmin Jahan Tithi
> PhD Student, CS
> Stony Brook University, NY-11790.
>
>
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