[gmx-users] Few queries about microsecond long simulations

[anu chandra]

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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