AMBER Archive (2005)

Subject: Re: AMBER: OH- dynamics

From: Eric Hu (eric.y.hu_at_gmail.com)
Date: Wed Mar 30 2005 - 18:23:32 CST

Yes, I understant that now. Thanks for your input.

Best,
-Eric

On Wed, 30 Mar 2005 18:37:26 -0500, Carlos Simmerling
<carlos_at_ilion.bio.sunysb.edu> wrote:
> well what it does is keep the only term in your energy function constant
> over the perturbation. look at the sander energy report- everything is
> zero but the bond term, and it isn't changing. that's why the derivative
> is zero. maybe that's what you wanted....
>
> Eric Hu wrote:
>
> >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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