RE: how to restart FEP

From: jia (
Date: Fri Oct 26 2007 - 15:29:12 CDT

Hi Jerome,

Thanks for the quick response. I intend to restart inbetween windows, but had
trouble with the configure file. Here is the FEP part in my NAMD configure
file, which is for all the windows, but there's no way to finish the
calculations in a single run, therefore I'd divide into multiple runs and
restart inbetween windows, and wonder if you could give me some hints on how
to do that. Thanks much.

source fep.tcl
fep on
fepFile S2A.fep
fepCol B
fepOutFreq 10
fepOutFile S2A.fepout

fepEquilSteps 20000

set nSteps 120000
set DLambda 0.1
set init { 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 }
runFEPlist $init $nSteps
runFEP 0.1 0.9 $dLambda $nSteps
runFEPlist $end $nSteps

I'm doing a mutation of Ser to Ala in a solvated system.


>===== Original Message From Jerome Henin <> =====
>Hello Jiancong,
>If you intend to restart inbetween windows (i.e. the last window is
>complete and you want to start a new one), a normal restart will do.
>The code does not directly support restarting in the middle of a
>window. If you do it, you will have to combine the data from the two
>half-windows by hand. The simplest way is to collect dE values (column
>7 in the fepout file), and combine them using the exponential formula.
>On 10/26/07, jia <> wrote:
>> Dear NAMD users,
>> I need to restart a FEP simulations, and I am wondering if there's anything
>> different from normal NAMD restart, or if it's necessary to provide a
>> different fepfile for the restart. I've looked up both the user's guide and
>> the tutorial, but just couldn't find the answer. Thanks much.
>> Jiancong

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