Hello Wes, I ran some more test simulations. I think the error is because I added counterions to neutralize my system (it has a +2 charge) prior to the free energy. Without the counterions, the simulations are running fine. Though, I don't know whether such a behavior is expected. Such a setup (with counterions) is not something unheard of.
Nevertheless, I read elsewhere that for solvation free energy calculation of charged system, the uniform background charge as implemented in PME for non-neutral systems may be desirable. Hence, I plan to run the simulations without counterions. Sincerely, Abhishek Abhishek Acharya Research Associate, Department of Molecular Nutrition CSIR-Central Food Technological Research Institute, Mysuru-570020 On Tue, Sep 12, 2017 at 5:22 PM, Wes Barnett <w.barn...@columbia.edu> wrote: > On Tue, Sep 12, 2017 at 12:17 AM, Abhishek Acharya < > abhi117acha...@gmail.com > > wrote: > > > Just to add to the above post, running a none to vdw-q tranformation > using > > the following parameters also results in the same error for simulation at > > first lambda. > > > > > Do you get this error on a normal simulation as well? That is, if you run > state 0 (with vdw and electrostatics on) without doing an free energy > calculations, do you still get the error? Perhaps you are using too big a > of a time step or your system is not equilibrated enough before using this > time step. Or you may just have a bad starting configuration. > > > > > > ************************************************************ > > ************************************************************ > > ******************************************************** > > vdw_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 0.40 > > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 > 1.00 > > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 > 1.00 > > 1.00 1.00 > > coul_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 > 0.15 > > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 > 0.90 > > 0.95 1.00 > > ; We are not transforming any bonded or restrained interactions > > bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > ; Masses are not changing (particle identities are the same at lambda = 0 > > and lambda = 1) > > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > ; Not doing simulated temperting here > > temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > 0.00 > > 0.00 0.00 > > ; Options for the decoupling > > sc-alpha = 0.5 > > sc-coul = no ; linear interpolation of Coulomb > (none > > in this case) > > sc-power = 1 > > sc-sigma = 0.3 > > couple-moltype = Protein ; name of moleculetype to decouple > > couple-lambda0 = none > > couple-lambda1 = vdw-q > > couple-intramol = no > > nstdhdl = 10 > > ************************************************************ > > ************************************************************ > > ******************************************************** > > > > Thanks in advance. > > > > Abhishek Acharya > > Research Associate, > > Department of Molecular Nutrition > > CSIR-Central Food Technological Research Institute, > > Mysuru-570020 > > > > On Tue, Sep 12, 2017 at 9:42 AM, Abhishek Acharya < > > abhi117acha...@gmail.com> > > wrote: > > > > > Hello GROMACS users, > > > > > > As Wes had advised previously in this thread, the issue with the vdw > > > tranformations was rectified by removing the charges from the topology > > > file. Thereafter, I also tried running free energy calculations using > the > > > following free-energy parameters: > > > > > > ************************************************************ > > > ************************************************************ > > > ******************************************************** > > > free_energy = yes > > > init_lambda_state = 0 > > > delta_lambda = 0 > > > calc_lambda_neighbors = 1 ; only immediate neighboring > windows > > > ; Vectors of lambda specified here > > > ; Each combination is an index that is retrieved from for each > simulation > > > coul_lambdas = 0.00 0.05 0.10 0.15 0.20 0.25 0.30 0.35 > 0.40 > > > 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 0.90 0.95 1.00 1.00 1.00 > > 1.00 > > > 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 > > 1.00 > > > 1.00 1.00 > > > vdw_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.05 0.10 > > 0.15 > > > 0.20 0.25 0.30 0.35 0.40 0.45 0.50 0.55 0.60 0.65 0.70 0.75 0.80 0.85 > > 0.90 > > > 0.95 1.00 > > > bonded_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 > > > restraint_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 > > > mass_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 > > > temperature_lambdas = 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 > > 0.00 > > > 0.00 0.00 > > > ; Options for the decoupling > > > sc-alpha = 0.5 > > > sc-coul = no ; linear interpolation of Coulomb > > > (none in this case) > > > sc-power = 1 > > > sc-sigma = 0.3 > > > couple-moltype = Protein ; name of moleculetype to decouple > > > couple-lambda0 = vdw-q > > > couple-lambda1 = none > > > couple-intramol = no > > > nstdhdl = 10 > > > > > > ************************************************************ > > > ************************************************************ > > > ******************************************************** > > > > > > As you can see, I want to first annihilate the charges, followed by a > vdw > > > tranformation, using a total of 41 lambdas. Since both charges and vdw > > are > > > being interpolated, the topology files contain the normal charges for > the > > > transformed molecule. This setup is similar to what Wes had suggested > in > > a > > > previous response to this thread. > > > > > > The issue is that I am facing the exactly the same error in > minimization > > > step at final lambda state where both vdw and electrostatics are turned > > off. > > > > > > ------------------------------------------------------------ > > > ------------------------------------------------------------ > > > ------------------------------------------------------ > > > Program gmx mdrun, VERSION 5.1.2 > > > Source code file: /home/bp-lab/Downloads/gromacs-5.1.2/src/gromacs/ > > mdlib/constr.cpp, > > > line: 555 > > > > > > Fatal error: > > > > > > step 10: Water molecule starting at atom 120 can not be settled. > > > Check for bad contacts and/or reduce the timestep if appropriate. > > > > > > For more information and tips for troubleshooting, please check the > > GROMACS > > > website at http://www.gromacs.org/Documentation/Errors > > > > > > ------------------------------------------------------------ > > > ------------------------------------------------------------ > > > ------------------------------------------------------- > > > > > > Now, what I understood is that in case of just the vdw transformation, > > > since we are not calculating any electrostatics, the charges should be > > zero > > > in topology file. Whereas, in case of just the charge transformation, > the > > > charges are required in the topology file as charges are interpolated > in > > > this step. And performing the simulation as such give no errors. > > > > > > I do not understand why the error is surfacing in case of a [vdw-q] to > > > [none ] tranformation., especially now that the charges are gradually > > > decoupled prior to decoupling the vdw interactions. Any help will be > > > greatly appreciated. > > > > > > Sincerely, > > > Abhishek > > > > > > > > > Abhishek Acharya > > > Research Associate, > > > Department of Molecular Nutrition > > > CSIR-Central Food Technological Research Institute, > > > Mysuru-570020 > > > > > > On Sun, Sep 10, 2017 at 8:02 AM, Abhishek Acharya < > > > abhi117acha...@gmail.com> wrote: > > > > > >> > > >> > > >> > > >> You can do them separately, but the charges need to have been turned > off > > >> for the molecule you are transforming for the second step when turning > > off > > >> vdw. In other words, all charges must be 0.0 for the molecule in the > > >> topology file for the vdw transformation. Is that what you've done? > > >> > > >> Justin's tutorial gives an explanation on why this needs to be done, > and > > >> in > > >> his topology he had all charges at 0.0 in the methane topology file. > > >> > > >> > > >> Okey, one thing that I presumed while performing the second > > >> transformation is that it is sufficient to 'turn-off' charge > > electrostatics > > >> just by stating c-lambda0=none and c-lambda1 = vdw (or vice-versa). It > > >> doesn't matter if the topology files have the charges or not. > > Therefore, i > > >> had included the charges in my topology file. > > >> > > >> Then this explains the problem in my case. Thank you so much Wes for > > >> clarifying that out. > > >> > > >> Sincerely, > > >> Abhishek Acharya > > >> > > >> > > >> > > > > > -- > > 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. > > > > > > -- > James "Wes" Barnett > Postdoctoral Research Scientist > Department of Chemical Engineering > Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> > Columbia University > w.barn...@columbia.edu > http://wbarnett.us > -- > 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.
