AMBER Archive (2005)

Subject: Re: AMBER: OH- dynamics

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Wed Mar 30 2005 - 16:03:53 CST

Ok, when I set nscm = 0, the problem is solved. Thank you. However
there is no DV/DL value during the perturbation. Here are my frcmod
file and the summary of the TI output. -Eric

remark goes here
MASS
OH 16.000 0.465 same as oh
HO 1.008 0.135 same as ho
DO 16.000 0.465 same as oh
DH 1.008 0.135 same as ho

BOND
OH-HO 369.60 0.974 same as ho-oh
DO-DH 369.60 0.974 same as ho-oh

ANGLE

DIHE

IMPROPER

NONBON
  OH 1.7210 0.2104 same as oh
  HO 1.0000 0.0000 same as ho
  DO 1.0000 0.0000 same as oh
  DH 1.0000 0.0000 same as ho

      A V E R A G E S O V E R 20000 S T E P S

 NSTEP = 20000 TIME(PS) = 20.000 TEMP(K) = 269.63 PRESS = 0.0
 Etot = 3.3569 EKtot = 1.6074 EPtot = 1.7495
 BOND = 1.7495 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S

 NSTEP = 20000 TIME(PS) = 20.000 TEMP(K) = 225.14 PRESS = 0.0
 Etot = 1.2220 EKtot = 1.3422 EPtot = 1.4609
 BOND = 1.4609 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000
 ------------------------------------------------------------------------------

      DV/DL, AVERAGES OVER 20000 STEPS

 NSTEP = 20000 TIME(PS) = 20.000 TEMP(K) = 0.00 PRESS = 0.0
 Etot = 0.0000 EKtot = 0.0000 EPtot = 0.0000
 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 0.0000
 EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT = 0.0000

On Wed, 30 Mar 2005 14:14:07 -0500, Carlos Simmerling
<carlos_at_ilion.bio.sunysb.edu> wrote:
> I don't think you'll be able to use nscm in this case....
>
>
> Eric Hu wrote:
>
> >Hi, I want to do a OH- dynamics is vaccum and water. I got the
> >following error in vaccum:
> >
> >%CENMAS-F-INERTIA_TENSOR, determinant is zero ... stop
> >
> >I suspect that this is caused by the linearity of OH-. How do I get
> >around this error? Thanks.
> >
> >
> >Eric
> >
> > title here
> >&cntrl
> > ntr=0,
> > nstlim =20000, nscm=2000, ntave=5000,
> > ntx=1, irest=0, ntb=0, cut=99, ntpr=100, tempi=300.0, ig=974651,
> > ntp=0, taup=1.0,
> > dt=0.001, nrespa=1,
> > ntt=1, temp0 = 300., tautp=2.0,
> > ntc=2, ntf=2, tol=0.000001,
> > ntwr = 10000, ntwx=0,
> > icfe=1, clambda=0.04691,
> >
> >/
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