From: Chris Harrison (charris5_at_gmail.com)
Date: Fri Apr 20 2012 - 19:34:48 CDT
At a minimum, try implementing a SASA measurement using tcl via the
tclForces interface. Going thru VMD to do this is, as Axel put it, is
insanity for practical aspects of performance. You'll actually spend
less time writing and testing the tcl SASA script than you would
running the simulation if you pursue your original idea. If your tcl
implementation performs accurately it might form the basis for
something we could later convert into actual code within NAMD. But
please, for the love of doing things the smart way, try first to
calculate your SASA via a tcl script that runs via the tclForces
interface and updates the forces.
On Fri, Apr 20, 2012 at 7:04 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Apr 20, 2012 at 7:14 PM, Ajith Rathnaweera Rajapaksha Mudalige
> <arajapak_at_purdue.edu> wrote:
>> Thanks Alex, Aron,
>> Yes, practically I will want to update the forces after every 500 time steps or so.
>> I know this will slow down the simulation but it is an essential step to run the simulation correctly.
>> The forces I am applying to my system is depending on Solvent Accessible Surface (SAS) of the molecule. SAS can be determined using "measure SASA" command in VMD. This is not directly supported in NAMD (please correct me if I am wrong). Therefore, I need to run the simulation in NAMD load the current phase in VMD and determine SAS at that point, determine the direction of the forces, get back to NAMD and run for the next phase.
>> Is this possible?
> sure, but how many times do i need to repeat it?
> just implement a SASA measurement into NAMD.
> that would be *far* less work than everything else.
> what you propose to do is insanity.
>> I will highly appreciate if anyone can give me a little concrete example, if anyone has done this type of a work before.
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
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