Re: [AMBER] Converting Gromacs coordinate file to Amber input files formolecular dynamics

From: Vlad Cojocaru <vlad.cojocaru.mpi-muenster.mpg.de>
Date: Wed, 21 Mar 2012 18:10:52 +0100

Hi Adam

I am not sure this is a good idea ...
Do you have a good reason for changing the software in the middle of the simulation?

If you do have a good reason, I would think you need some sort of equilibration to adapt your system to the new software... So I dont think you can simply continue the same simulation but rather start a new one ... Well, anyhow I dont see any good reason why you want to continue same simulation with different software ...

You can convert gro to pdb using vmd for example ... Maybe ptraj also reads gro but not sure ...

Vlad

---
Dr. Vlad Cojocaru
Max Planck Institute Muenster
Roentgenstrasse 20,
48149 Muenster, Germany
Tel: +49-251-70365324
Sent from my mobile phone; Sorry for being short and for any errors
Adam Jion <adamjion.yahoo.com> wrote:
Hi!
I have the coordinate file (.gro) of a Gromacs simulation box (i.e. protein solvated in water).
Can I convert this file into something that can be used as input for molecular dynamics simulation in Amber?
Regards,
Adam
ps. I have simulated the system in Gromacs for ~ 100 ns, and wish to continue the same simulation in Amber
pps. The simulation in Gromacs uses an Amber force-field. So blow-ups are unlikely.
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Received on Wed Mar 21 2012 - 10:30:02 PDT