Tutorial-l Mailing List

From: sharvil kaware (sharvil_kaware_at_yahoo.co.in)
Date: Thu Mar 04 2010 - 20:10:52 CST

Good morning everybody.
I am trying to simulate( using NAMD) 5nm   dia  water droplet transition to 2nm dia  droplet  by evaporation and subsequent visualization by VMD.
Since last 6 months I have been struggling to simulate 5nm diameter  only water sphere , enclosed in 6nm side water box using periodic boundary conditions and completed several simulation runs.I  want to simulate water nanodroplet evaporation at around 373K and expecting to see gradual  evaporation of sphere to smaller size sphere(many be 2-3 nm dia).Will I be able to see such transition after 10ps or more (may be 1ns) simulation? and can I count density/number of  water molecules in certain radius from centre of sphere? Also, I am using cell basis vector(x,y z)  of 8nm from cell origin to provide vapor surrounding to my system.is it ok?
Please guide me  on this issue.I will be very much thankful to you and your team for guidance.

Thank You,
With High Regards
Ravindra Kaware
Ph.D. candidate,North Carolina A &T State University 
Greensboro, NC USA

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