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 <bipinel...@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 <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. -- 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.