Hi:
Okay..I was thinking that this might require a source code modification. Perhaps I could consult you, or Prof. Roitberg as needed?
Best, Jerome
-----Original Message-----
From: Ross Walker [mailto:ross.rosswalker.co.uk]
Sent: Wednesday, December 01, 2010 1:39 PM
To: 'AMBER Mailing List'
Subject: Re: [AMBER] (no subject)
Hi Jerome,
The value of lambda is fixed during the TI simulation so there is no way to
modify it during a simulation without getting your hands dirty. One 'hack'
would be to run a few hundred steps and stop writing a restart file and then
start again with a new lambda value, wash, rinse, repeat. This could be
easily scripted in a shell script although the performance will not be great
as you will have to pay the startup penalty on each restart.
A cleaner way would be to modify the source code to change the value of
lambda. I haven't looked into it but this should not be too hard to change,
just trace it through from where it is first read from the namelist to find
where one would change it. In principal this would work. The question that
may need thinking about is whether it is valid to do this. Is simply
changing lambda ok or is there some gradient with respect to lambda that you
would need to take into account. This will need some thinking about while
looking at the equations so you might want to consider that first.
In summary you will need to modify the code but it shouldn't be too
difficult assuming there are not some strange derivatives that have to be
taken into account.
All the best
Ross
> -----Original Message-----
> From: Nilmeier, Jerome P. [mailto:nilmeier1.llnl.gov]
> Sent: Wednesday, December 01, 2010 1:20 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] (no subject)
>
> Hello:
>
> I am interested in applications very similar to what a steered md run
might
> provide, but with alchemical parameters as the time varying function. I
am
> just now learning the details of Amber, and I thought that maybe there
> would be a way to generate these types of trajectories using existing
> machinery. Perhaps we can talk more about it when you have time?
>
> Best, J
>
> -----Original Message-----
> From: Adrian Roitberg [mailto:roitberg.qtp.ufl.edu]
> Sent: Wednesday, December 01, 2010 8:10 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] (no subject)
>
> I am pretty sure there is no code like that in amber, but I would be
> VERY interested in why you would do such a thing.
>
> Adrian
>
> On 12/1/10 5:05 PM, case wrote:
> > On Tue, Nov 30, 2010, Nilmeier, Jerome P. wrote:
> >
> >> I am interested in generating trajectories whereby an alchemical
> >> potential is continuously altered over the course of the trajectory.
> >> (Something like steered MD, but with lambda varying rather than a
> >> biasing potential). Is there a straightforward way to do this?
> >
> > I'm pretty sure there is no current way to do this, unless Volodymyr
stuck
> > something in the ABMD stuff that I missed....
> >
> > ...dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
> --
> Dr. Adrian E. Roitberg
> Associate Professor
> Quantum Theory Project, Department of Chemistry
> University of Florida
>
> Senior Editor. Journal of Physical Chemistry.
>
> on Sabbatical in Barcelona until August 2011.
> Email roitberg.ufl.edu
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Dec 01 2010 - 14:00:03 PST
