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On 23/05/2011 10:38 PM, Mikhail Stukan wrote:
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<p class="MsoNormal"><span style="font-family:
"Arial","sans-serif"; font-weight:
normal;">Dear gmx-users,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:
"Arial","sans-serif"; font-weight:
normal;"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:
"Arial","sans-serif"; font-weight:
normal;">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? </span></p>
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<br>
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.<br>
<br>
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.<br>
<br>
Mark<br>
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