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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Received on Mon Jul 09 2012 - 14:30:03 PDT
