AMBER Archive (2002)

Subject: Re: box size & 1st equilibrium

From: Carlos Simmerling (carlos.simmerling_at_sunysb.edu)
Date: Fri Jun 28 2002 - 06:56:09 CDT

try using a much smaller force constant for restraints.
something like 1.0 should work just fine and still
be a strong restraint.
Carlos

----- Original Message -----
From: "yuann" <yuann_at_bioinfo.ndhu.edu.tw>
To: <amber_at_heimdal.compchem.ucsf.edu>
Sent: Friday, June 28, 2002 2:16 AM
Subject: box size & 1st equilibrium

> Dear AMBER users:
> I've encountered blow up problem when I do a dynamics run
> (1st equilibrium) with constant pressure PBC's. (I'd like to
> equilibrate the density of mysystem: (DNA+WAT+Na+) generated by Leap).
> The error message is:
> COORDINATE RESETTING CANNOT BE ACCOMPLISHED,
> DEVIATION IS TOO LARGE
>
> Weirdly, it just appears when I turn on NTR with force restrain(500),
> and the dynamics job works smoothly with turning on ibelly.
> However, I'm warned in mdout when using ibelly, and ibelly doesn't seem
> to be suitable for DNA...?
>
> I also checked the vdw bounding box of solute & whole box as follows,
>
> > solvatebox dna WATBOX216 {3.7, 3.5, 3.8} 1.0
> Solute vdw bounding box: 27.702 33.472 44.833
> Total bounding box for atom centers: 35.102 40.472 52.433
> Solvent unit box: 18.774 18.774 18.774
> Total vdw box size: 37.968 43.772 55.471 angstroms.
> Volume: 92188.719 A^3
> Total mass 39673.368 amu, Density 0.715 g/cc
> Added 1792 residues.
>
> The cut off distance is 9A. I took notice of the same problem in
> this Mail Reflector Archive, so I also edited the vdw in the bottom of
> inpcrd file by increasing 3A to each axis. The error message above was
> still appeared at around 13ps(the density is still < 1).
>
> Thanks for your help!
>
> Best Regards,
> sychen
>
> (here is the mdin of this dynamics job)
> -------------------------------------------------
> &cntrl
> imin=0, dt=0.002, ntr=1, ntb=2, nstlim=10000,
> irest=0, ntx=1, t=0.000,
> ntc=2, tol=0.0005, ntf=2,
> ntt=1, temp0=100.0, tempi=0.0, tautp=1.0,
> ntp=1, taup=0.2,
> cut=9.0,
> ntpr=50, ntwr=50, ntwx=50,
> &end
> Group input for restrained DNA
> 500
> RES 1 24
> END
> END
>
>