From: Aron Broom (broomsday_at_gmail.com)
Date: Fri Apr 20 2012 - 23:46:53 CDT
As a kind of crazy side point here, doesn't the NAMD implicit solvation
code utilize a Linear Combination of Partial Overlaps (LCPO) code to
calculate not only SASA, but also uses that to generate a force in order to
minimize SASA?
I may be totally off base on that.
~Aron
On Fri, Apr 20, 2012 at 9:28 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> On Fri, Apr 20, 2012 at 9:19 PM, Ajith Rathnaweera Rajapaksha Mudalige
> <arajapak_at_purdue.edu> wrote:
> > Hi Axel,
> >
> > measure sasa has other capabilities...
> >
> > It can compute the points on the solvent accessible surface and this can
> be done for each individual atoms.
> > Forces are calculated using the coordinates of these points. So when the
> forces are in action surface changes and therefore forces are to be updated.
>
> ok. i wasn't looking a the argument list of the code only at the return
> value.
>
> > Everything I need can be done in NAMD, except computing measure sasa.
> >
> > Any suggestions?
>
> if this is the case, passing the data from NAMD to VMD
> and back is EVEN MORE STUPID, if that is at all possible.
>
> why on earth do you insist on this insanity?
> the SASA algorithm is not very difficult.
> running two executables in step and
> communicating data between them is,
> not to mention the insane overhead of
> formatting numbers into text, communicating
> them and then parsing it and converting
> to Tcl and back.
>
> axel.
>
> >
> > Ajith
> >
> > ----- Original Message -----
> > From: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
> > To: "Ajith Rathnaweera Rajapaksha Mudalige" <arajapak_at_purdue.edu>
> > Cc: "Aron Broom" <broomsday_at_gmail.com>, namd-l_at_ks.uiuc.edu
> > Sent: Friday, April 20, 2012 8:42:49 PM
> > Subject: Re: namd-l: Simulation Using Both NAMD and VMD
> >
> > On Fri, Apr 20, 2012 at 7:14 PM, Ajith Rathnaweera Rajapaksha Mudalige
> > <arajapak_at_purdue.edu> wrote:
> >> Hi
> >>
> >> 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.
> >
> > wait...
> >
> > there is one more thing that doesn't add up. measure sasa gives
> > your a single number: the area. how does this compute into a
> > directional force?
> >
> > axel.
> >
> >>
> >> Is this possible?
> >>
> >> I will highly appreciate if anyone can give me a little concrete
> example, if anyone has done this type of a work before.
> >>
> >> Regards,
> >>
> >> Ajith
> >>
> >>
> >>
> >>
> >> ----- Original Message -----
> >> From: "Aron Broom" <broomsday_at_gmail.com>
> >> To: "Axel Kohlmeyer" <akohlmey_at_gmail.com>
> >> Cc: "Ajith Rathnaweera Rajapaksha Mudalige" <arajapak_at_purdue.edu>,
> namd-l_at_ks.uiuc.edu
> >> Sent: Friday, April 20, 2012 6:30:14 PM
> >> Subject: Re: namd-l: Simulation Using Both NAMD and VMD
> >>
> >> Is it possible to use the tcl forces capability of NAMD to run the
> script you want? As Axel points out, passing the information into VMD at
> every timestep would be crippling (unless your simulation takes an
> extremely long time per timestep already). If you only need to update the
> forces every 1000 timesteps or something, that might work.
> >>
> >> ~Aron
> >>
> >>
> >> On Fri, Apr 20, 2012 at 6:10 PM, Axel Kohlmeyer < akohlmey_at_gmail.com >
> wrote:
> >>
> >>
> >>
> >> On Fri, Apr 20, 2012 at 6:05 PM, Ajith Rathnaweera Rajapaksha Mudalige
> >> < arajapak_at_purdue.edu > wrote:
> >>> Hi Everybody,
> >>>
> >>> Is it possible to write a script for a NAMD simulation to access VMD
> at each time step through Interactive Molecular Dynamics mode (or any other
> possible way).
> >>
> >> technically yes. in practice no, since that would be highly inefficient.
> >> better to implement what you need into NAMD directly.
> >>
> >> axel.
> >>
> >>
> >>
> >>> In my simulation I need to execute some VMD commands at each time step
> and define a new force according to the results output from VMD.
> >>>
> >>> I highly appreciate if someone could shed some light in this direction.
> >>
> >>
> >>
> >>
> >>> Regards,
> >>>
> >>> Ajith
> >>>
> >>
> >>
> >>
> >> --
> >> Dr. Axel Kohlmeyer
> >> akohlmey_at_gmail.com http://goo.gl/1wk0
> >>
> >> College of Science and Technology
> >> Temple University, Philadelphia PA, USA.
> >>
> >>
> >>
> >>
> >> --
> >> Aron Broom M.Sc
> >> PhD Student
> >> Department of Chemistry
> >> University of Waterloo
> >
> >
> >
> > --
> > Dr. Axel Kohlmeyer
> > akohlmey_at_gmail.com http://goo.gl/1wk0
> >
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
>
>
>
> --
> Dr. Axel Kohlmeyer
> akohlmey_at_gmail.com http://goo.gl/1wk0
>
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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