Nadeem,
Thanks. I increased my Ethreshp and started seeing numbers under
dV_Epot and fwgt* Epot. Makes me happy.
Any idea about the zeros at ntwx? Looks like a possible bug.
On Mon, Jul 9, 2012 at 4:03 PM, Nadeem A. Vellore <vnadeem.gmail.com> wrote:
> Dear Milo,
>
> The amd.log is read with this information.
>
>
>> Col1 col2 Epot DIH fwgt* Epot fwgt* DIH dV_Epot dV_DIH
> 500 500 1 33.8569 88.16073 1.0000000
> 0.2096640 0.00000 8.075207538317
>
>
> dV_DIH is the dihedral biasing potential applied based on the Current
> dihedral potential calculated.
> Since the energy is more than the threshold, you get a zero biasing
> for potential energy.
>
>
>
> Nadeem
>
> ===================
> Nadeem Ahmad Vellore
> Dept. of Medicinal Chemistry
> University of Utah, SLC
> ===================
>
>
>
>
> On Mon, Jul 9, 2012 at 1:48 PM, Milo Westler <milo.nmrfam.wisc.edu> wrote:
>> I have a question about the output file, amd.log, from an aMD run. I
>> am using a dual-boost aMD run (iamd=3) using pmemd.cuda on a M2090 GPU
>> under Amber 12. Here is the input script:
>>
>>
>> aMD stage 1
>> &cntrl
>> ig=-1,
>> imin=0, irest=1, ntx=5,
>> nstlim=50000, dt=0.002,
>> ntc=2, ntf=2,
>> ntt=3, gamma_ln=2, tautp=1.0,
>> tempi=400.0, temp0=400.0,
>> ntpr=500, ntwx=500,
>> ntb=0, igb=5,
>> cut=999.,rgbmax=999.
>> iamd=3,EthreshD=100,alphaD=10,EthreshP=0.7120,alphaP=14,
>> /
>>
>> I find it curious that the amd.log file looks like:
>>
>> 500 500 1 33.856868858000
>> 88.160733387000 1.000000000000 0.209664015720
>> 0.000000000000 8.075207538317
>> 500 500 2 34.716339958000
>> 88.197373083000 1.000000000000 0.210369295934
>> 0.000000000000 8.038789872964
>> 500 500 3 35.383199675000
>> 88.130778395000 1.000000000000 0.209090041690
>> 0.000000000000 8.105005110879
>>
>> The fwgt (column 6), which I interpret as the boost for the potential
>> energy, is always at 1.00 and the tboostall (column 8) are always
>> zero.
>>
>> Another curiosity is that for the line that equals the ntwx value I
>> always get all zeros (I have tried this with different ntwx values):
>>
>> 500 500 500 0.000000000000
>> 0.000000000000 0.000000000000 0.000000000000
>> 0.000000000000 0.000000000000
>>
>> If this output is correct, what am I missing? It would seem to me that
>> there should be a force and boost value for the potential and I really
>> am confused as to why the values are all zero in the last instance.
>>
>> Thanks,
>>
>>
>> --
>> -- Milo
>> ===================================================
>> National Magnetic Resonance Facility at Madison
>> An NIH-Supported Resource Center
>>
>> W. Milo Westler, Ph.D.
>>
>> NMRFAM Director
>> Senior Scientist
>> and
>> Adjunct Professor
>> Department of Biochemistry
>> University of Wisconsin-Madison
>> 433 Babcock Drive
>> Madison, WI USA 53706-1544
>> EMAIL: milo.nmrfam.wisc.edu
>> PHONE: (608)-263-9599
>> FAX: (608)-263-1722
>> ======================================================================= ========
>>
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>
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--
-- Milo
===================================================
National Magnetic Resonance Facility at Madison
An NIH-Supported Resource Center
W. Milo Westler, Ph.D.
NMRFAM Director
Senior Scientist
and
Adjunct Professor
Department of Biochemistry
University of Wisconsin-Madison
433 Babcock Drive
Madison, WI USA 53706-1544
EMAIL: milo.nmrfam.wisc.edu
PHONE: (608)-263-9599
FAX: (608)-263-1722
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Received on Mon Jul 09 2012 - 18:00:02 PDT
