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.scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo.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.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Apr 29 2005 - 00:53:01 PDT
