Re: Protein moving out of water-box after 10 ns simulation

From: Per Jr. Greisen (pgreisen_at_gmail.com)
Date: Wed Feb 27 2008 - 09:40:49 CST

You should probably read the section on wrap-coordinates. That should fix
your problem.
Hope it helps
Best

On Wed, Feb 27, 2008 at 3:13 PM, Jie-rong Huang <jierongh_at_googlemail.com>
wrote:

> Dear NAMD users,
>
> I run a script (as used in tutorial) with 10 ps minimization and then run
> for 10 ns for ubiquitin with 15 Na and 15 Cl randomly added by "Add Ions"
> plug-in. However, in the end of 10 ns, part of the protein came out of the
> water-bax (I used "solvate" with layer 8A). How I can keep the protein in
> the middle of water box during the long trajectory simulation? Only way I
> can think about is put
>
> fixedAtoms on
> fixedAtomsForces on
> fixedAtomsFile ubiquitin.pdb #column B of a few residue (maybe 1 or 2)
> are "1"
> fixedAtomsCol B
>
> However, this "going-out" problem might only be caused by some parameter
> setting.....
> Can anyone give me some suggestions?
>
> Jie-rong

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