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

[bipin singh]

Thank you Prof. Shirts for your help and suggestions.


On Sat, Nov 30, 2013 at 6:04 AM, Michael Shirts <mrshirts at gmail.com> wrote:

> The fluctuation is often of the order of magnitude of <dh/dl> itself.
> It's <dh/dl> that matters.
>
>
>
> On Thu, Nov 28, 2013 at 1:26 PM, bipin singh <bipinelmat at gmail.com> wrote:
> > 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*
> >> > --
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> >
> >
> >
> > --
> >
> >
> >
> > *--------------------Thanks and Regards,Bipin Singh*
> > --
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-- 



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