[gmx-users] Regarding soft core parameter: Relative solvation free energy calculation

[bipin singh]

Thanks for you reply Prof. Shirts.

I have plotted the dh/dl values (link mentioned below), but I am not sure
whether the fluctuation is in acceptable range at lambda=0.0. Please have a
look at the plot and let me know your thoughts.

http://researchweb.iiit.ac.in/~bipin.singh/dhdl.png


On Thu, Nov 28, 2013 at 8:44 PM, Michael Shirts <mrshirts at gmail.com> wrote:

> It's very possible that this is entirely physical. dh/dl fluctuates a
> lot.  You may want to look at graphs of <dh/dl> after a few 10's of ps
> to see if it looks reasonable.
>
> On Thu, Nov 28, 2013 at 10:04 AM, bipin singh <bipinelmat at gmail.com>
> wrote:
> > I am mentioning below the average and standard deviation of dh/dl values
> at
> > lambda=0.0 and lambda=1.0, for sc-alpha=0.5
> >
> >                             Avg             Std.
> >  lambda0.0    -2.055812e+01   2.730571e+01
> >
> >  lambda1.0    7.086960e+01    7.670135e+00
> >
> >
> > On Thu, Nov 28, 2013 at 7:34 PM, bipin singh <bipinelmat at gmail.com>
> wrote:
> >
> >> Thanks for the reply.
> >>
> >> By large fluctuations, I mean the standard deviation of dh/dl values
> >> during the simulation at lambda 0.0 to 0.5 in comparison to lambda
> close to
> >> 1, when using sc-alpha=0.5
> >>
> >>
> >> On Thu, Nov 28, 2013 at 7:27 PM, Michael Shirts <mrshirts at gmail.com
> >wrote:
> >>
> >>> Define large fluctuations.  They might be physical large fluctuations!
> >>>
> >>>
> >>>
> >>> On Thu, Nov 28, 2013 at 1:19 AM, bipin singh <bipinelmat at gmail.com>
> >>> wrote:
> >>> > Hello All,
> >>> >
> >>> > I am trying to calculate relative solvation free energy for p-Cresol
> and
> >>> > p-Chlorophenol using Gromacs 4.6.3.
> >>> >
> >>> > I am using equispaced lamda values viz. 0.1, 0.05, 0.1,...., 1.0
> >>> >
> >>> > During one transformation (lambda 0.0 to 1.0) I am switching off the
> vdW
> >>> > terms (Changed to DUM atoms) for the -CH3 and -Cl group in p-Cresol
> amd
> >>> > p-Chlorophenol respectively.
> >>> >
> >>> > Thus I am using a constant sc-alpha=0.5 at each lambda values (0.0 to
> >>> 1.0)
> >>> > for both the molecules.
> >>> >
> >>> > But I am getting a large fluctuation in dh/dl values only at initial
> >>> lambda
> >>> > values i.e. from 0.0 to 0.5, and only in the case of p-Cresol (-CH3
> is
> >>> > being changed to DUM).
> >>> >
> >>> > If I change the sc-alpha=0 for initial lamda ( i.e. from 0.0 to
> 0.5), I
> >>> get
> >>> > consistent values of dh/dl (i.e. less deviation during simulation).
> >>> >
> >>> >
> >>> > Can anyone suggest the reason for this behaviour and how to select
> >>> > appropriate values of sc-alpha based on transformation. And can we
> use
> >>> > different sets of sc-alpha values for two molecules to compute their
> >>> > relative solvation free energies.
> >>> >
> >>> >
> >>> > ############################################
> >>> > I have used the following mdp settings:
> >>> >
> >>> > sc-power                 = 1
> >>> > sc-alpha                 = 0.5
> >>> > sc-r-power               = 6
> >>> > sc-coul                  = no
> >>> >
> >>> >
> >>> > and
> >>> >
> >>> >
> >>> > sc-power                 = 1
> >>> > sc-alpha                 = 0.0
> >>> > sc-r-power               = 6
> >>> > sc-coul                  = no
> >>> >
> >>> > ###############################################
> >>> >
> >>> >
> >>> >
> >>> >
> >>> >
> >>> > *--------------------Thanks and Regards,Bipin Singh*
> >>> > --
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> >>
> >>
> >>
> >> --
> >>
> >>
> >>
> >> *--------------------Thanks and Regards, Bipin Singh*
> >>
> >>
> >
> >
> > --
> >
> >
> >
> > *--------------------Thanks and Regards,Bipin Singh*
> > --
> > Gromacs Users mailing list
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-- 



*--------------------Thanks and Regards,Bipin Singh*