[gmx-users] Regarding soft core parameter: Relative solvation free energy calculation
Michael Shirts
mrshirts at gmail.com
Sat Nov 30 01:34:57 CET 2013
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*
> --
> Gromacs Users mailing list
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