[gmx-users] Few queries about microsecond long simulations

[anu chandra]

Many thanks for your suggestions.

On Tue, Aug 18, 2015 at 12:52 PM, Ganesh Shahane <ganesh7shahane at gmail.com>
wrote:

> Hi Anu,
>
> 1) It really depends on what kind of analysis you are doing. If you are,
> for example, studying bio-molecular interactions that take place over
> microsecond long timescales then saving trajectories every 200-500 ps is
> advisable. I myself do receptor-membrane atomistic simulations with a
> saving frequency of 500 ps. You don't really need saving which is as
> frequent as 10 ps.
>
> 2), 3) Whereas .xtc trajectories contain only the coordinates, .trr
> trajectories contain both coordinates as well as velocities. So unless you
> are going to do any analysis which involves the velocities of
> atoms/particles, its safe to not write-out the .trr file. Still you are
> never really sure if you are going to require velocities or not and so it's
> best to write out the .trr file as well.
>
> On Tue, Aug 18, 2015 at 4:30 PM, Felipe Merino <
> felipe.merino at mpi-dortmund.mpg.de> wrote:
>
> > Hi,
> >
> > 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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>
>
> --
> Best Regards,
> Ganesh Shahane
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