First meeting with NAMD

From: James Starlight (
Date: Mon Jun 03 2013 - 09:08:58 CDT

Dear NAMD users!

Recently I've tried to launch my first simulation on NAMD :) (previously
I've used Gromacs ).
My questions:

1) Typical gromacs simulation consist of energy minimization +
equilibration in NPT ensemble (with position restraints applied on each
atoms of protein) + production run.

As I understood minimization should explicitly defined in the conf file

# Minimization
minimize 100
reinitvels $temperature

run 5000000

but what about equilibration stage ? How I can perform short simulation
with the applied porses prior to the production run?

2) How I can monitor total performance of the GPU utilized in the
simulation assuming that I use CUDA.

3) I have parameters ( prm and inp files) for some non-standard residue (
GFP chromophore). for this protein I'd like to make model (including
protein covalently bonded to the chromophore and solvent) and perform
simulation. Could you provide me with the example or short tutorial for
such task?

Thanks for help,


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