[gmx-users] Fwd: -pbc nojump

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Oct 27 13:59:21 CEST 2010

Hi Leila,

2.xtc should contain all that you want.
My point was that you shouldn't need to separate protein/dna and
solvent into two trajectories to be combined later.
Note that this only concerns visualization. You can do distance and
H-bond calculations on the original trajectory, as the relevant tools
know how to deal with PBC.



On Wed, Oct 27, 2010 at 12:01 PM, leila karami <karami.leila1 at gmail.com> wrote:
> Dear Carsten and David and Tsjerk
> Thanks for your time and attention
> My purpose of these questions is to find a way that 1) close two separated
> strand of dna (in my case only –pbc nojump fix it) and also 2) water
> molecules to be put in interface of between protein and dna. Because I want
> to survey interfacial water molecules and dynamics of water mediated
> hydrogen bonds.
> --
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Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
The Netherlands

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