AMBER Archive (2005)

Subject: AMBER: vlimit

From: Gustavo Pierdominici Sottile (gsottile_at_unq.edu.ar)
Date: Fri Mar 11 2005 - 06:33:36 CST

Hi ,
    When heating from 0 K to 300 K , it allways appeared the problem of
vlimit as soon as the dynamic process begun. I found the reason of the
problem, but not the solution. With the starting protein in pdb , I use the
solvateCap keyword of leap to solvate the system. If the heating is done
without water molecules, there is no problem. Moreover, if the heating is
done with water molecules constraining them, the is no problem too. If the
constraint is small , the problem appears but not as soon as the dynamic
starts. It can be also seen that, as the constraint increases , the vlimit
problem appears later.
In conclusion , the problem is the movement of water molecules. How can I do
to run the dynamic of the system with solvent, but letting water molecules
move without leaving the ball?
Can I rise the density of the molecules of the box?
Is it possible to constrain only those molecules that are in the surface?
Thanks in advance
Gustavo

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