AMBER Archive (2002)

Subject: RE: md equilibration in chloroform

From: Thomas.Fox_at_bc.boehringer-ingelheim.com
Date: Thu Jul 11 2002 - 12:51:47 CDT

...its been a while since I did the chloroform parametrizations, so I might
not remember all
the details correctly, and some problems might have gone away with more
recent
versions of amber...just a number of remarks:
1) equilibration of and in CHCl3 took quite a while, definitely much longer
than in water,
    especially when using a flexible CHCl3 model
2) I remember having had some problems with the 'flying ice cube'
phenomenon,
    you might want to check that (this probably also depends on your choice
of thermostat, though)
3) I think I used a compressability of 9.74 10^10 m^2/N, but I cant access
my input files
    anymore...maybe there's something in our paper on non-aqueous solvents (
Fox&Kollman JPC 1997/98)
    In any case, as Dave pointed out, it doesnt matter what number you put
in...
4) The shake error usually points to a rather bad initial configuration of
the solvent atoms...how did you build
    your CHCl3 box? Either increasing the initial distance between the
chloroforms, or just manually
    adding a couple of A to your box dimensions in the input files might
help...
5) In my experience, its perfectly valid to start out with constant pressure
- I think I never used constant energy
    before constant pressure PDB. You just have to make sure that your
solvent molecules start out with
    enough space - otherwise you get either this notorious SHAKE error
message, or a completely blown up
    box which takes forever to come back to reasonable densities...

Th.

> Dr. Thomas Fox
> Dept. Chemical Reseach / Structural Research
> K91-00-10
> Boehringer Ingelheim Pharma KG
> 88397 Biberach/Germany
> Thomas.Fox_at_bc.boehringer-ingelheim.com
>
>
> -----Original Message-----
> From: David A. Case [SMTP:case_at_scripps.edu]
> Sent: Monday, July 08, 2002 5:42 PM
> To: Sophia Kondratova
> Cc: amber_at_heimdal.compchem.ucsf.edu
> Subject: Re: md equilibration in chloroform
>
> On Mon, Jul 08, 2002, Sophia Kondratova wrote:
>
> > I am having difficulties equilibrating a ligand/receptor complex in a
> > chloroform box. I need to equilibrate the system to 300K in an NPT
> ensemble
> > with SHAKE. What value of COMP(compressibility of the system) should I
> be
> > using? ( 700 chcl3 in the box, 50.7410000 49.2030000 50.8920000
> dimensions)
> > If anyone has done chloroform simulations, maybe they could tell me what
>
> > parameters are used to correctly equilibrate a chloroform box. Should I
> > equilibrate first using an NVT ensemble? The error message that I get
> when I
> > try to equilibrate:
> >
> > Coordinate resetting (SHAKE) cannot be accomplished,
> > deviation is too large
> > NITER, NIT, LL, I and J are : 0 3 2956 3651 3649
> >
> > Note: This is usually a symptom of some deeper
> > problem with the energetics of the system.
> >
>
> For any type of solvent, you must equilibrate at constant volume to room
> temperature before trying to do constant pressure simulations.
>
> It doesn't matter much what you put in for the compressibility: this just
> interacts with the time constant (taup) to determine how quickly the
> volume
> adjusts to the instantaneous pressure. Using the water value should work
> OK.
>
> ..good luck....dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================