**From:** Shyno Mathew (*sm3334_at_columbia.edu*)

**Date:** Tue Dec 03 2013 - 17:12:43 CST

**Next message:**vapour: "Re: Phosphorylating a residue with Amber ff"**Previous message:**Giacomo Fiorin: "Re: Colvars periodic boundary treatment question"**In reply to:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Next in thread:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Reply:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

Hello Jerome,

Is there a way to make sure my system is equilibrated at each strata?

Currently, I do 10000 steps of equilibration followed by 10000 steps of

data collection. But I am not sure 10,000 steps of equilibration is enough?

Also, what method/algorithm namd uses to do FEP?

I read BAR is another method to calculate free energy.

Since the ParseFEPplugin was showing us some errors, we are trying to write

a script that calculates BAR.

thanks,

Shyno

On Fri, Nov 22, 2013 at 1:09 PM, Shyno Mathew <sm3334_at_columbia.edu> wrote:

*> Hi Jerome,
*

*> I was using "minimize" incorrectly.
*

*> I meant for each window I have 5000 steps of equilibration followed by
*

*> 10,000 steps of data collection.
*

*> So I should try increasing the equilibration steps.
*

*>
*

*> thanks,
*

*> Shyno
*

*>
*

*>
*

*>
*

*> On Fri, Nov 22, 2013 at 12:01 PM, Shyno Mathew <sm3334_at_columbia.edu>wrote:
*

*>
*

*>> thanks again Jerome. Sorry to bother with multiple questions.
*

*>> Here is how the FEP section of my .conf file looks like (I saw it in one
*

*>> of the FEP tutorials).
*

*>> So for each window it does 5000 step minimization followed by 10,000 step
*

*>> run. What you are suggesting is just do minimization at the very first
*

*>> window only?
*

*>>
*

*>> alch on
*

*>> alchType FEP
*

*>> alchFile 04collab_wet.fep
*

*>> alchCol B
*

*>> alchOutFile 05collab.fepout
*

*>> alchOutFreq 100
*

*>> alchVdwLambdaEnd 1.0
*

*>> alchElecLambdaStart 0.5
*

*>> alchVdWShiftCoeff 5.0
*

*>> alchDecouple off
*

*>> alchEquilSteps 5000
*

*>>
*

*>> set Lambda0 0.0
*

*>> set dLambda 0.05
*

*>> while {$Lambda0 < 1.0} {
*

*>> alchLambda $Lambda0
*

*>> set Lambda0 [expr \$Lambda0 + \$dLambda]
*

*>> alchLambda2 $Lambda0
*

*>> run 15000
*

*>> }
*

*>>
*

*>> thanks,
*

*>> Shyno
*

*>>
*

*>>
*

*>>
*

*>> On Fri, Nov 22, 2013 at 11:49 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr>wrote:
*

*>>
*

*>>> ----- Original Message -----
*

*>>> > Thanks for the reply Jerome.
*

*>>> > Now, for each window I have 5000 minimization followed by 10000 steps--001a11c3f0420f27e804eca96f30--
*

**Next message:**vapour: "Re: Phosphorylating a residue with Amber ff"**Previous message:**Giacomo Fiorin: "Re: Colvars periodic boundary treatment question"**In reply to:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Next in thread:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Reply:**Shyno Mathew: "Re: FEP calculations: optimizing the dlambda, number of steps"**Messages sorted by:**[ date ] [ thread ] [ subject ] [ author ] [ attachment ]

*
This archive was generated by hypermail 2.1.6
: Tue Dec 31 2013 - 23:24:03 CST
*