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.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.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,
>>>>>
>>>>>/
>>>>>-----------------------------------------------------------------------
>>>>>The AMBER Mail Reflector
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
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>>>>
>>>>
>>>>
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Received on Thu Mar 31 2005 - 00:53:00 PST
