[gmx-users] Few queries about microsecond long simulations

Felipe Merino felipe.merino at mpi-dortmund.mpg.de
Tue Aug 18 13:01:02 CEST 2015


This are all questions that mostly only you can answer.
On 18/08/15 12:42, anu chandra wrote:
> Dear Gromcas users,
> I am planning to do microsecond long simulation of membrane-protein system
> and I have ~100,000 atoms in the systems. Since I am trying for microsecond
> long simulations and I have a quiet large system, it can generate large
> amount of data and in this regard I would like to clarify few queries
> before continue the simulations. My queries are,
> 1. How often I should save the trajectories? In general, I have seen that
> mostly use 2ps interval for saving trajectories, as shown below. Will it be
> safe if I use 10ps ( 5000 steps ) interval for saving trajectories?
> nstxout         = 1000          ; save coordinates every 2 ps
> nstvout         = 1000          ; save velocities every 2 ps
> nstenergy       = 1000          ; save energies every 2 ps
> nstlog          = 1000          ; update log file every 2 ps
The files you create and the frequency with which you write them depends 
only on what you want to measure in the end. In principle, you want to 
save every couple of decorrelation times, for whatever property 
interests you. I assume that since you want a microsecond-long 
simulation then you are going for a slow process and therefore you don't 
need so frequent saving. Just as a comparison, for one of my simulations 
(~550k atoms, 1 µs) I save the coordinates every 40 ps which gives me a 
final xtc of ~50Gb of space.
> 2. How safe if I just write only the compressed .xtc file of the
> trajectories and not the .trr file during the production run? If its safe,
> how can I tell mdrun not to write the trr file?
> 3. Do I really need the trr file for any MD analysis?
Again, you should know if you need the velocities later, or if need a 
high precision for the coordinates. If you don't, then leave the mdp as,
nstxout         = 0
nstvout         = 0
nstenergy       = 1000
nstlog          = 1000
nstxtcout   = 1000
> Many thanks in advance
> Anu

Felipe Merino
Max Planck Institute for Molecular Physiology
Department of Structural Biochemistry
Otto-Hahn-Str. 11
44227 Dortmund
Phone: +49 231 133 2306

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