On 12/27/2011 5:38 PM, Nidhi Katyal wrote:
Dear all,
I am trying to create tmao box.Energy minimization, simulated
annealing (Cooling under
high pressure and again heating at normal pressure) as well as final
equilibration ran smoothly.
But finally I got a box where all water molecules got accumulated in
two three small region within the box
and tmao molecules in another small regions.I wanted near random
uniform distribution of tmao in water.
Perhaps the box didn't get equilibrated properly.
Any help from user, where I am wrong and what should I do.
Your SA protocol sounds like a recipe for problems. See
http://www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation
The usual process for generating a box of mixed solvents is here
http://www.gromacs.org/Documentation/How-tos/Mixed_Solvents but your
cosolvent may be too large for the genbox -ci replacement procedure.
Then, you may need to use the ideas here
(http://www.gromacs.org/Documentation/How-tos/Non-Water_Solvation) to
make a suitably dilute TMAO solution that can then be "solvated" with
water with genbox -cs. Either way, lengthy equilibration will be in order.
Mark
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