[gmx-users] NAMD simulation in Gromacs

Mark Abraham mark.abraham at anu.edu.au
Thu Sep 30 13:55:04 CEST 2010

----- Original Message -----
From: oguz gurbulak <gurbulakoguz at yahoo.com>
Date: Thursday, September 30, 2010 21:38
Subject: [gmx-users] NAMD simulation in Gromacs
To: gmx-users at gromacs.org

|   > Dear All,
  > I performed a 50 ns md simulation using NAMD and want to continue this simulation for 10 ns in Gromacs. Is it possible to continue a NAMD simulation in Gromacs ? If so, could you please give me the information about this process ? 

Not really. You would need to generate a .top in the normal way, and this process cannot use any topology information that NAMD was using. You could start the GROMACS simulation from the endpoint of the NAMD simulation, but it would not be continuous in any sense.

  Secondly can I convert NAMD output files into gromacs output files and use gromacs analysis tools ? Could you please also give me the information about this issue ?
If you have VMD installed then GROMACS is supposed to be able to link to its libraries to enable GROMACS tools to read any file format that VMD can read, which will include all NAMD formats. I'm unaware that anybody has written any documentation about this, however. That's probably the path of least resistance.



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