The fluctuation is often of the order of magnitude of <dh/dl> itself. It's <dh/dl> that matters.
On Thu, Nov 28, 2013 at 1:26 PM, bipin singh <bipinel...@gmail.com> wrote: > Thanks for you reply Prof. Shirts. > > I have plotted the dh/dl values (link mentioned below), but I am not sure > whether the fluctuation is in acceptable range at lambda=0.0. Please have a > look at the plot and let me know your thoughts. > > http://researchweb.iiit.ac.in/~bipin.singh/dhdl.png > > > On Thu, Nov 28, 2013 at 8:44 PM, Michael Shirts <mrshi...@gmail.com> wrote: > >> 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-usersor >> >>> 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. >> > > > > -- > > > > *--------------------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.