Please, disregard my last message. I've found the answer here
http://archive.ambermd.org/201303/0027.html
But now I have another question. My amd.log file looks like this,
1000 1000 1 -244983.961652883328 5150.554060385000
0.877386849692 1.000000000000 122.560169373394
0.000000000000
1000 1000 2 -245258.279528016457
4908.733101503000 0.864339807604 0.000000000000
152.255951286500 230.274951345411
1000 1000 3 -245595.981875224505
4786.527299220000 0.844405798738 0.000000000000
204.922763049394 435.283846299278
1000 1000 4 -245589.265768913552
4795.329286301000 0.844216231486 0.000000000000
205.467551961184 420.517889114242
Now, as I understand it, the weighting factor should be the exponential of
1/kT times (column_8+column_9), am I right?
If that's so I'm getting some pretty gigantic numbers for exp(\beta
\deltaV). For the last line it would be exp((205+420)/0.59)=10^271 which is
a somewhat ridiculous number. Am I calculating the reweighting factor
wrong, or should I try to reduce (a lot) the boosting potential by changing
my aMD parameters?
Also, if I calculate \DeltaVp=(EthreshP-col4)^2/(alphaP+EthreshP-col4) I
don't get column 8, nor do I get column 9 if I calculate \DeltaVd using
column 5 and the corresponding EthreshD and alphaD parameters. For example,
for row 1:
\DeltaVp= (-243830 + 244983.9)^2/(17073 - 243830 + 244983.9) = 73 != 122.56
What am I missing?
PS: My system consists of a 600 aminocids protein with a total 900000 atoms
including water molecules. EthreshP=-243830 alphaP=17073, EthreshD=5046
and alphaD=444 Kcal/mol.
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Received on Tue Apr 16 2013 - 16:30:03 PDT
