From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Thu Dec 12 2013 - 03:05:30 CST
Did you enable a barostat?
Jerome
----- Original Message -----
> to make my question more clear:
> I have a cubic water box, but as the FEP progresses, shape of the water box
> becomes more irregular.
> All the water molecular are still there, but boundaries look more distorted!!
> On Wed, Dec 11, 2013 at 4:00 PM, Shyno Mathew < sm3334_at_columbia.edu > wrote:
> > Hi all,
>
> > Initially while doing FEP, I wasn't outputting the dcd file!!
>
> > Now, I did a short run with dcdfreq specification. When I look at the
> > trajectory, I see the water box is chopped little on each corner.
>
> > In the beginning the water box looks fine (rectangular shape). As FEP
> > progresses, some water molecules are disappearing.
>
> > Does this mean something is wrong with the FEP calculations I did?
>
> > Look forward to hearing an answer!!
>
> > thanks,
>
> > Shyno
>
> > On Tue, Dec 10, 2013 at 11:28 AM, Shyno Mathew < sm3334_at_columbia.edu >
> > wrote:
>
> > > Dear all,
> >
>
> > > I would like to confirm the FEP part in my .conf file is correct?
> >
>
> > > 1. Here is how it looks like for the forward FEP :
> >
>
> > > 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 $Lambda0
> >
>
> > > run 15000
> >
>
> > > }
> >
>
> > > 2. Now for the reverse FEP everything is same except the following:
> >
>
> > > set Lambda0 1.0
> >
>
> > > set dLambda -0.05
> >
>
> > > while {$Lambda0 > 0.0}
> >
>
> > > thanks in advance for your help,
> >
>
> > > best,
> >
>
> > > Shyno
> >
>
> > > On Tue, Dec 3, 2013 at 6:12 PM, Shyno Mathew < sm3334_at_columbia.edu >
> > > wrote:
> >
>
> > > > 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.
> > > > > > > > I
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > > did try going to 10^6 steps, but didn't give significant
> > > > > > > > difference
> > > > > > > > in
> > > > > > > > free
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > > energy.
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > In general I wouldn't recommend minimizing between windows. You
> > > > > > > have
> > > > > > > to
> > > > > > > thermalize to room temperature again every time, and discard the
> > > > > > > additional
> > > > > > > equilibration time.
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > > So just to be clear, in the previous message by saying
> > > > > > > > "increase
> > > > > > > > the
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > > sampling time for just those two by running extra simulations"
> > > > > > > > you
> > > > > > > > meant
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > > going to smaller dlambda values between 0.45 and 0.55?
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > I meant running more MD for the same lambda and dlambda values.
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > > Also, does it make sense to do FEP just between 0.45 and 0.55
> > > > > > > > and
> > > > > > > > then
> > > > > > > > use
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > > it with data for all other windows?
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > Yes, you can merge any amount of data from separate runs. How to
> > > > > > > do
> > > > > > > it
> > > > > > > properly depends on what free energy estimator you use. For the
> > > > > > > FEP
> > > > > > > estimator, it's just a matter of taking the log of a weighted
> > > > > > > average
> > > > > > > of
> > > > > > > exponenials of deltaGs.
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > > Jerome
> > > > > >
> > > > >
> > > >
> > >
> >
>
> > > > > > --
> > > > >
> > > >
> > >
> >
>
> > > > > > Shyno Mathew
> > > > >
> > > >
> > >
> >
>
> > > > > > PhD student
> > > > >
> > > >
> > >
> >
>
> > > > > > Department of Chemical Engineering
> > > > >
> > > >
> > >
> >
>
> > > > > > Columbia University
> > > > >
> > > >
> > >
> >
>
> > > > > --
> > > >
> > >
> >
>
> > > > > Shyno Mathew
> > > >
> > >
> >
>
> > > > > PhD student
> > > >
> > >
> >
>
> > > > > Department of Chemical Engineering
> > > >
> > >
> >
>
> > > > > Columbia University
> > > >
> > >
> >
>
> > > > --
> > >
> >
>
> > > > Shyno Mathew
> > >
> >
>
> > > > PhD student
> > >
> >
>
> > > > Department of Chemical Engineering
> > >
> >
>
> > > > Columbia University
> > >
> >
>
> > > --
> >
>
> > > Shyno Mathew
> >
>
> > > PhD student
> >
>
> > > Department of Chemical Engineering
> >
>
> > > Columbia University
> >
>
> > --
>
> > Shyno Mathew
>
> > PhD student
>
> > Department of Chemical Engineering
>
> > Columbia University
>
> --
> Shyno Mathew
> PhD student
> Department of Chemical Engineering
> Columbia University
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