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 <mrshi...@gmail.com> wrote: > Define large fluctuations. They might be physical large fluctuations! > > > > On Thu, Nov 28, 2013 at 1:19 AM, bipin singh <bipinel...@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 > > > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- *--------------------Thanks and Regards,Bipin Singh* -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
