[gmx-users] Few queries about microsecond long simulations

Ganesh Shahane ganesh7shahane at gmail.com
Wed Aug 19 11:46:36 CEST 2015


Hi Anu,

Since .xtc doesn't store velocities, its a much more compact trajectory
than it's .trr counterpart, i.e. it has a smaller size. Also, .xtc is more
easier on your computer RAM than the .trr file, during visualizing or
analyzing using the .xtc trajectories.

If you are looking to save disk space and if you won't need the velocities,
output only the xtc file.

On Wed, Aug 19, 2015 at 2:57 PM, anu chandra <anu80125 at gmail.com> wrote:

> Hi Felipe and Ganesh,
>
> Do we really need to save coordinates in both of these two formats - trr
> and .xtc?. If one save the .trr file, what is the need of .xtc file since
> .trr can provide all the informations required with higher precision. All I
> am looking for is to save some disk space.
>
> Thanks
> Anu
>
> On Tue, Aug 18, 2015 at 3:19 PM, anu chandra <anu80125 at gmail.com> wrote:
>
> > 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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-- 
Best Regards,
Ganesh Shahane


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