[gmx-users] Velocity and temperature profiles

[Mark Abraham]

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.

Mark
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