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

[bipin singh]

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*