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.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.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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>>>
>>>
>>>
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Received on Wed Mar 30 2005 - 23:53:01 PST
