**From:** jesmin jahan (*shraban03_at_gmail.com*)

**Date:** Wed Dec 05 2012 - 09:52:15 CST

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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:**Thomas Evangelidis: "aMD with implicit solvent - Segmentation fault"**Previous message:**David Minh: "Re: How to compute "only the GB Energy" using NAMD?"**In reply to:**jesmin jahan: "How to compute "only the GB Energy" using NAMD?"**Next in thread:**David Minh: "Re: How to compute "only the GB Energy" using NAMD?"**Reply:**David Minh: "Re: How to compute "only the GB Energy" using NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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