On Wed, 2014-04-09 at 13:32 -0400, Christopher A Thiebaut wrote:
> I'm pretty sure I know the source of the degrees of freedom
> discrepancy. I have several other similar systems (also thermolysin,
> same box size, different ligands) which I am also going to simulate.
> They don't all have an identical number of water molecules, but the
> results would be easier to summarize/interpret if they were all run at
> the same temperatures. I assumed that since the variance in the
> number of water molecules/degrees of freedom was small compared to the
> total number that the effect of that difference on the exchange
> probability would be negligible. Was that a very flawed assumption?
Most likely. You can use either cpptraj or ParmEd to strip away 'extra'
waters so each system has the same number of atoms if you must use the
same temperature ladder. I suspect you will get almost precisely your
target 22% acceptance on the system that has the same number of
particles you put into the REMD generator worksheet.
If the same temperature ladder gives you wildly different acceptance
rates for another system, then the difference in the degrees of freedom
is (almost) certainly the culprit.
That said, your original post said:
> > > These temperatures are based on 102229 degrees of freedom for the
> system
> > > and a desired exchange probability of .22. According to my mdout
> files,
> > > the system actually has 101423 degrees of freedom. So I think the
Since each rigid water adds only 1 additional degree of freedom, you
have an extra 800 water molecules in some system compared to the input
you gave to the REMD generator. This is quite a bit...
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Apr 09 2014 - 11:00:05 PDT
