Help in FEP backward/reverse calculation

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Thu Sep 22 2011 - 14:36:38 CDT

Dears NAMD users,

I am performing a FEP calculation using NAMD and the dual topology aproach. I would like to estimate the difference in the binding energy between some Rhenium complexes and the corresponding ligands (compounds without the metal Re(CO)3 part; flag -1 in the fep.tcl to vanish).

I did the foward transformation and the calculated results are in good agreement with the experimental results.

Now I need to calculate the backward transformation to monitor the hysteresis.

Here comes my first doubt (I have little experience with FEP that´s why I am asking for your help).

For the bacward transformation I need to use the files otbained from the forward transformation (forward_0.coor, forward.coor, forward.vel, etc...) Am i right???

Another doubt:

If my forward input is:

alchEquilSteps 8000
set nSteps 40000

set dLambda 0.1

set init {0.0 0.0000001 0.000001 0.00001 0.0001 0.001 0.01 0.05 0.1}
set end {0.9 0.95 0.99 0.999 0.9999 0.99999 0.999999 0.9999999 1.0}

runFEPlist $init $nSteps
runFEP 0.1 0.9 $dLambda $nSteps
runFEPlist $end $nSteps

My backward input should be:

alchEquilSteps 8000
set nSteps 40000

set dLambda 0.1

set init {0.9 0.95 0.99 0.999 0.9999 0.99999 0.999999 0.9999999 1.0}
set end {0.0 0.0000001 0.000001 0.00001 0.0001 0.001 0.01 0.05 0.1}

runFEPlist $init $nSteps
runFEP 0.9 0.1 $dLambda $nSteps
runFEPlist $end $nSteps

Than the backward simulation followed the same setup with the exception of the fep.tcl file where the fags are 1 for the Re(CO)3. That´s it??

Can anybody help me, please ???!!!

Thank you in advance.

Bruno
...................................................................................................................................................
Bruno L. Oliveira
Radiopharmaceutical Sciences Group
Chemistry Department , ITN
http://www.itn.pt/sec/qui/qir/uk_qir_index.htm
http://www.boliveira.com

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