AMBER Archive (2005)

Subject: Re: AMBER: A problem in TI approach - test case: meth2eth and eth2meth

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Thu Apr 28 2005 - 18:34:48 CDT

Hi Petr,

Thanks for your suggestion. I am using Langevine Dynamics, and I thought
that it is using canonical ensemble. I am not sure if mass is important in
canonical ensembles, because the configurations created does not depend on
the mass. What I mean is that the probability of observing a system in
some position 'r' (in any momentum) is mass independent in canonical
ensembles.

Best,

On Thu, 28 Apr 2005, Petr Kulhanek wrote:

> Hello,
>
> >I am thinking that the reason for this difference lies in the perturbation
> >I am intended. In one case (meth->eth), I am changing a proton to a
> >carbon, and in another one (eth->meth), I am changing a carbon to a
> >proton. This might be the reason why I am getting such a difference.
> >(Maybe the method I am following is no good for creating/annihilating
> >heavy atoms) So, I will test my 'new' sander to a case where I am
> >creating/annihilating just protons.
> >
> I have one remark related to your problem. Format of AMBER topology is
> not able to reflect mass changes in perturbation calculations. It means
> that if you change a carbon to a proton, only force field parameters
> (bond lengths, ...) are changed but mass not. This could be the
> explanation of observed differences. To solve this problem, you should
> use dummy atoms.
>
>
> Petr Kulhanek
>
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
> 

-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
  ---------------------------------------------------------------

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu