On 17/02/2012 4:46 PM, James Starlight wrote:
So my problem still is
1) During npt without peptide my Ccl4 system expan rapidly in
X-dimension. That produce error on 2nd ns of equilibration
One of the box vectors has become shorter than twice the cut-off
length or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
2) During npt with peptide my system expan rapidly in Z direction (
along that axe my peptide is oriented) So as concequence I've obtained
the same error.
What does a cube of CCl4 do? If it is not stable at an acceptable
density then your parameters don't work at all. Starting with simple
things and adding complexity gradually is always a good policy, even
when you're an expert. There's so many things that can be slightly wrong...
Possible sollution wich I've found in litterature
1) To fix one dimension of my PB. How I could fix the X dimension of
my box during npt phace of pure Ccl4 and allow only change in 2 other
dimensions ?
See pcoupltype in manual 7.3.15
2) I have not found radius for Cl for Gromos56 ff.
Is this possible to decrease that value during npt phase to obtain
system with desired hight density? What value should I use?
As someone else said, the radius is only material during things like
genbox. In the simulation, your nonbonded parameters are the important
thing.
Mark
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