[gmx-users] (no subject)

[Mark Abraham]

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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