Dear Amber users,
I would like to simulate an aqueous solution containing benzyltriethyl
ammonium chloride. I put 30 cation molecules and 30 Cl- ions in a box
with the edge of 80 A. The system is solvated with TIP3P water
molecules, using the tleap command:
SolvateBox A TIP3PBOX 0
Where A is the name of the box containing the solute.
I use the following simulation protocol:
1) 2000 cycle minimization with restrain on the solute;
2) 3500 cycle minimization on the entire system;
3) 20 ps of simulated annealing in order to reach the temperature of 300 K;
4) 100 ps of pressure equilibration, in order to reach the correct
density and a pressure of 1 atm;
5) 10 ns dynamics;
After pressure equilibration, I am not able to obtain the correct
density since I have an underestimated value of 0.98.
Do you have some suggestion to solve this problem?
I thank you in advance.
Tommaso
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Received on Wed Jul 06 2011 - 03:30:03 PDT
