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

[Michael Shirts]

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*
>>> > --
>>> > Gromacs Users mailing list
>>> >
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>>
>>
>>
>> --
>>
>>
>>
>> *--------------------Thanks and Regards, Bipin Singh*
>>
>>
>
>
> --
>
>
>
> *--------------------Thanks and Regards,Bipin Singh*
> --
> Gromacs Users mailing list
>
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