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.