**From:** David Minh (*daveminh_at_gmail.com*)

**Date:** Wed Dec 05 2012 - 09:56:09 CST

**Next message:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Previous message:**Axel Kohlmeyer: "Re: AW: Simulation Box Deformation"**In reply to:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Next in thread:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Reply:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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.
*

*>
*

*>
*

**Next message:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Previous message:**Axel Kohlmeyer: "Re: AW: Simulation Box Deformation"**In reply to:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Next in thread:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Reply:**jesmin jahan: "Re: How to compute "only the GB Energy" using NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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