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

Michael Shirts mrshirts at gmail.com
Thu Nov 28 14:58:02 CET 2013


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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