[gmx-users] Velocity and temperature profiles
Mark.Abraham at anu.edu.au
Mon May 23 16:04:48 CEST 2011
On 23/05/2011 10:38 PM, Mikhail Stukan wrote:
> Dear gmx-users,
> I am currently working on a fluid flow in a nano-channel and would
> like to build velocity and temperature profiles across the channel.
> Could anyone give me a hint if it is possible to do this using the
> existing set of GROMACS tools?
Possible, but not easy. So long as you save simulation velocities in
your trajectory file, you'd then have to do some tedious scripting of
g_select to select suitable atoms for each point in your profile for
each trajectory snapshot. Then for each selection from each snapshot
you'd have to construct a matching topology to prepare a subset run
input file to match with a subset of a trajectory frame to pass to mdrun
-rerun to measure the local temperature of the subset.
This temperature might mean even less than a normal MD "temperature".
See Eastwood, M. P., Stafford, K. A., Lippert, R. A., Jensen, M. O.,
Maragakis, P., Predescu, C., Dror, R. O., Shaw, D. E. Equipartition and
the calculation of temperature in biomolecular simulations. J. Chem.
Theory Comp. ASAP:DOI: 10.1021/ct9002916, 2010.
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