AMBER Archive (2005)

Subject: Re: AMBER: OH- dynamics

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Wed Mar 30 2005 - 16:50:03 CST

I thought "DO-DH 369.60 0.974 same as ho-oh" would just do
that, wounldn't it?

Eric

On Wed, 30 Mar 2005 17:32:09 -0500, Carlos Simmerling
<carlos_at_ilion.bio.sunysb.edu> wrote:
> Eric,
> in the gas phase perturbation, nothing is changing
> in your setup. The atoms don't have any nonbond interaction
> since they are bonded, and you aren't changing the bond parameters.
> So, the energy of your system doesn't depend on lambda and
> therefore dV/dL is zero. This means you can just look at
> the solvated TI run.
>
> ===================================================================
> Carlos L. Simmerling, Ph.D.
> Associate Professor Phone: (631) 632-1336
> Center for Structural Biology Fax: (631) 632-1555
> Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
> Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
> ===================================================================
>
>
> Eric Hu wrote:
>
> >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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