Re: vmd-l: dummy atoms and FEP

From: Peter Freddolino (
Date: Thu Apr 06 2006 - 11:45:26 CDT

Dear Raul,
it is pretty easy to set the Na charge to zero: Open your system's psf
file in a text editor, find the line corresponding to your sodium atom
(you can look by index or look for something called "Na"), and change
the 7th column (which contains the charge) to 0.000000. The NAMD
tutorial has some good general information on psf files that may be
helpful in figuring out how to do something like this.

Raul Araya Secchi wrote:

> Dear NAMD users
> Im still fighting with the FEP....but new quiestions arise all the
> time....
> I need to make a Na ion dissapear from my system to keep it neutral
> (for PME) but I dont know if I should put just a DUM atom (using the
> charmm 22 parameters and topologies) with 0 charge 0 mass or a Na ion
> without charge (dont know well how to do this). The reason for my
> question is that I only need the charge to dissapear in my FEP, ant
> the DUM atom has tha radii of the H atom I think....
> Is that simple, replace the Na for a DUM or it requires some other trick?
> please Help
> And again: Have any one used or is familiar with the Overlap Sampling
> method for FEP? or the Bennet method?
> thanks
> Raul Araya
> CGB-Universidad Catolica de Chile
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