[gmx-users] Re: freeze dummy atom completely

Pim Schravendijk schraven at mpip-mainz.mpg.de
Fri Aug 13 15:54:34 CEST 2004

Ok I found a brute-force solution, I changed my dummy atom topology to the
one shown below. It works, but is not very elegant :) What is the maximum
mass I can give without gromacs running into troubles somewhere?

[ moleculetype ]  
dumm              3

[ atoms ]
     1        DUM      1    DUMM   DUM      1    0.00000   99999999999999.00000 

Greetings, Pim

Pim Schravendijk - PhD Student
Max Planck Institute for Polymer Research

On Fri, 13 Aug 2004, Pim Schravendijk wrote:

> Hello,
> I am doing a simulation where a molecule-dummy atom z-distance is kept
> constant and I want to look at the potential of mean force depending on
> this distance. The dummy atom should be fixed at an absolute z-point in my
> box, x and y are not important.
> My problem is that, if I look at snapshots, my dummy atom doesn't remain
> at its z-position, it gets pushed away.  I guess the problem
> might be the mass of the dummy, I tried making it 0 but then grompp warns:

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