[gmx-users] Few queries about microsecond long simulations
ganesh7shahane at gmail.com
Tue Aug 18 13:52:48 CEST 2015
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:
> 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
>> 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
>> 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
> 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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