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 <bipinel...@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 <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* > > -- *--------------------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.