OK, in another thread with a similar question it was suggested that the
boosting energy was in units of kT, dividing \DeltaVp/0.59 (kT=0.59=0.0019
Kcal/mol K * 300 K) it renders 122.56.
My first question remains though. I'm getting to enormous exponential
weighting factors. Am I calculating them wrong or are the aMD parameters I
chose, bad?
Thanks a lot in advance. Any help will be greatly appreciated.
Diego Alonso de Armiņo
PhD student.
Tucuman National University
Tucuman, Argentina
2013/4/16 Diego Javier Alonso de Armiņo <diegoarmino.gmail.com>
> 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 Wed Apr 17 2013 - 08:00:02 PDT
