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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Received on Mon Jul 09 2012 - 13:00:03 PDT
