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

**Date:** Thu Dec 06 2012 - 07:44:43 CST

**Next message:**Norman Geist: "NAMD CUDA 2.9 Performance drop compared to 2.8"**Previous message:**Huihui Liu: "ask for new toppar files for drude in NAMD2.9"**In reply to:**David Minh: "Re: How to compute "only the GB Energy" using NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hi David,

Thanks for your reply. Is there any way to get itemize running time? I

wanted to get the running time only for GB energy calculation part?

Actually I tried to get the difference of running time with GBIS on

and off. But then the running time I got using this way of GB energy

computation of NAMD seems to be larger than both Amber and Gromacs.

Can you or anyone tell me how to get the actual time to compute only

the GB-energy part?

Thanks,

Jesmin

On Wed, Dec 5, 2012 at 10:56 AM, David Minh <daveminh_at_gmail.com> wrote:

*> 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.
*

*>>
*

*>
*

-- Jesmin Jahan Tithi PhD Student, CS Stony Brook University, NY-11790.

**Next message:**Norman Geist: "NAMD CUDA 2.9 Performance drop compared to 2.8"**Previous message:**Huihui Liu: "ask for new toppar files for drude in NAMD2.9"**In reply to:**David Minh: "Re: How to compute "only the GB Energy" using NAMD?"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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