Hi all,
For me the reweighing procedure is not clear too. Can you please give some clear example? What kind of software is best to use?
It is obvious that a lot of people start to use aMD and some manual/examples will be extremely helpful.
All the best,
Filip
________________________________
From: diego alonso <diegoarmino.yahoo.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Wednesday, April 17, 2013 2:00 AM
Subject: Re: [AMBER] aMD question: How to read the amd.log file
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.
________________________________
From: Diego Javier Alonso de Armiño <diegoarmino.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Tuesday, April 16, 2013 6:56 PM
Subject: [AMBER] aMD question: How to read the amd.log file
Dear Amber community,
I'm trying Accelerated Molecular Dynamics (dual boost, amd=3) on my
system. I want to calculate (corrected) free energy surfaces for certain
pairs of coordinates.
According to what I've read, the reweighting procedure consists of
obtaining the histogram with the following equation
Hij = \sum_k \delta_ij Exp(\beta*\DeltaV)
where the sum is over all the frames k, \delta_ij is 0 if the frame "k" the
coordinates in question fall into bin (ij) and cero otherwise, \beta is
1/kT and \DeltaV is the biasing potential.
The problem is, the manual doesn't explain how to read the amd.log file.
What's the meaning of each of the nine columns of the amd.log file?
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Received on Tue Apr 16 2013 - 18:30:02 PDT
