AMBER Archive (2008)

Subject: Re: AMBER: Can sander provide ESP with PBC?

From: Khatcharin Siriwong (skhatcha_at_kku.ac.th)
Date: Wed Apr 23 2008 - 20:43:12 CDT

Dear Thomas,

Thank you very  much for your message. It would be useful if Amber (sander) can print out ESP during MD simulation. Please let me know or post in amber website if this is done.

Thank you,

Khatcharin




On April 24, 2008 1:39:13 AM ICT, "Thomas Steinbrecher" <steinbrt@scripps.edu> wrote:

Dear John, Katcharin,

Amber does not have the capability to log the ESP on atoms during a
simulation. I have written a little module that does compute the ESP (no
gradients though) in sander for another algorithm, which is not in the
amber CVS tree yet. If you are interested, we can see if this does what
you need and maybe write a little bugfix which would put that capability
into Amber.

Kind Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Mon, 21 Apr 2008, John Chodera wrote:

> Hi Khatcharin,
>
> I think I am trying to do something similar to what you describe. I
> don't believe AMBER can currently compute the electrostatic potential
> on specified atoms by manipulating input flags, but it obviously does
> compute the potential as part of the energy computation during normal
> execution.
>
> Specifically, I am trying to modify a version of AMBER10's sander
> module to also write out the electrostatic potential and its first and
> second derivatives (which includes information on the electric field
> and its gradient) at specified atoms when running with a fixed-charge
> forcefield using PME. We're interested in using this to compute
> spectroscopic observables like FTIR spectra, but you may find this
> useful for your own purposes as well.
>
> Does this sound like it would be helpful to you? I can let you know
> when we have something working (hopefully in the next few days), and
> then can give you a patchset to try. We couldn't really support it,
> but it might at least help you get started.
>
> Cheers,
>
> - John
>
> --
> Dr. John D. Chodera | Mobile : 415.867.7384
> Postdoctoral researcher, Pande lab | Lab phone : 650.723.1097
> Department of Chemistry, Stanford University | Lab fax : 650.724.4021
> http://www.dillgroup.ucsf.edu/~jchodera
>
> On 21/04/2008, Khatcharin Siriwong wrote:
>>
>>
>> Dear All,
>>
>> I am using amber9 and I have an MD trajectory generated by sander module. I
>> would like to calculate the energy of the system in each snapshot for some
>> resons. Is it posiple that sander (or another module) can provide the
>> electrostatic potential (ESP) on atoms by taking into account the periodic
>> boundary condition? If yes, what keyword should be used and do I need to
>> re-generate the trajectory?
>>
>> Thank you very much in advance.
>>
>> Regards,
>>
>> Khatcharin
>>
>>
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