AMBER Archive (2005)

Subject: Re: Re :AMBER: Holes in water

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Sat Mar 12 2005 - 12:13:06 CST

> this is where the holes/voids do form. In fact, after the belly stage of
> the NPT dynamics, the system is well equilibrated, with the volume
> shrinked exactly as in the manual - and then at the next stage - where I
> am using positional constraints (NTR=1; RESTRAINT_WT and RESTRAINTMASK
> parameters used - it is AMBER 8), the system again expands and holes form.
> It is constant pressure, as well here. Interestingly, when I am deleting
> the constraints from the input file (and set NTR to 0), the system does
> not expand and holes don't seem to emerge. So maybe there is some problem
> with the NTR=1 option? But I actually need constraints in my experiment,

I'm not so familiar with restraints, but if they are cartesian,
could they be re-expanding the solute? Since solute is scaled
down during belly dynamics when the box shrinks.

Bill
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