[gmx-users] Atoms get frozen with "Nose Hoover thermostat with Parrinello-Rahman barostat" for a system of an ion of charge +2 in flexible water molecules
Dear Gromacs users, I am having a very strange problem with "Nose Hoover thermostat with Parrinello-Rahman barostat" NPT simulations for a system of an ion of charge +2 in flexible water molecules. Flexible water is taken from J. Chem. Phys. 124, 024503 (2006); http://dx.doi.org/10.1063/1.2136877. The ion is [UO2]2+ with charge on U=2.5 and each O has -0.25. Atoms very soon get frozen after the simulation starts and they remain frozen, they do not move at all. Only simulation box oscillates, which causes atoms to oscillate little bit but they do not move at all. Pressure, temperature etc. all get messed up. Here is some output from g_energy: " Statistics over 41 steps [ 0. through 400. ps ], 3 data sets All statistics are over 40001 points Energy Average Err.Est. RMSD Tot-Drift --- Potential -23648.5 202891.04 -117.711 (kJ/mol) Temperature 306.6840.1108.192 -0.566776 (K) Pressure538.6254.489041.8 79.925 (bar) " I am using this "Nose Hoover thermostat with Parrinello-Rahman barostat" after a well equilibration configuration obtained with Berendsen's thermostat and barostat. This problem is happening only when Parrinello-Rahman barostat used with Nose Hoover thermostat. I also noted the following observations: If I change either one of the thermostat or barostat with Berendsen, frozen problem disappears. If I change flexible water to rigid water, problem disappears. If my system has no ion, no problem happens. If I play with cut offs, rlist, then also sometimes problem disappears. The problem is independent on the size of box and number of water molecules. As expected, Diffusion constant is very close to zero. Here is my input MDP file: integrator = md dt = 0.001 tinit = 0 nsteps = 40 nstcomm = 10 pbc = xyz ;constraint_algorithm= lincs ;constraints = all-bonds continuation= yes ; continuing from equilibrated NPT nstxout = 200 nstvout = 5 nstfout = 0 nstlog = 5000 nstenergy= 2000 nstxtcout= 0 xtc-precision= 1000 nstlist = 10 ns_type = grid rlist= 1.1 coulombtype = PME_switch rcoulomb_switch = 0.6 rcoulomb = 0.9 vdw-type = switch rvdw-switch = 0.6 rvdw = 0.9 DispCorr= EnerPres fourierspacing = 0.12 fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 pme_order = 6 ewald_rtol = 1e-6 optimize_fft= yes tcoupl = nose-hoover tc-grps = System tau_t = 2 ref_t = 298.15 pcoupl = Parrinello-Rahman pcoupltype = isotropic tau_p = 2.0 ; time constant, in ps ref_p = 1.0 ; reference pressure (in bar) compressibility = 4.5e-5; isothermal compressibility, bar^-1 gen_vel = no Any help will be highly appreciated. Please let me know if someone needs any additional information to solve this issue. Thanks, Surya Prakash Tiwari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] Simulation of a charged system
Thanks Mark for the reply. I didn't find anything in AMBER manual. I emailed the author of that paper. I have one more question: Whether *charged system correction term*(-(1/(8*epsilon_0*kappa^2*L^3))*(Sum over q^2)) has been implemented in the PME implementation of Gromacs. I am talking about the last term of eqn. 15 on page 8 of the following paper: Warren, G. L., & Patel, S. (2007). Hydration free energies of monovalent ions in transferable intermolecular potential four point fluctuating charge water: an assessment of simulation methodology and force field performance and transferability. The Journal of chemical physics, 127(6), 064509. doi:10.1063/1.2771550 Thanks. Regards, Surya Prakash Tiwari On Tue, Dec 6, 2011 at 23:15, Mark Abraham wrote: > On 7/12/2011 11:31 AM, Surya Prakash Tiwari wrote: >> >> Dear Gromacs users, >> >> I am simulating a charged system with periodic boundary conditions. My >> system has 506 water molecules and one ion. >> I am trying to calculate the free energy of an ion. >> I do not want to use any counter-ions to neutralize the system, >> because I don't have force-field between my ion and the counterion. >> >> In particular, I want to reproduce the following paper: >> Horinek, D., Mamatkulov, S. I.,& Netz, R. R. (2009). Rational design >> >> of ion force fields based on thermodynamic solvation properties. The >> Journal of chemical physics, 130(12), 124507. doi:10.1063/1.3081142 >> >> Their system is also charged, has one ion and 506 water molecules. >> They are using AMBER software. On page number 7, they have discussed >> the correction terms due to ewald summation (equation 6) in a charaged >> system. >> On the same page, they further say that AMBER has implemented first >> term in eqn. 6 to account for ion’s Coulomb interaction with its >> periodic images: >> "In the PME implementation in AMBER, a self-energy correction of >> N*e^2 *xi /(8*pi*epsilon) is already accounted for." >> >> I just want to know whether, Gromacs has the same implementation in >> their PME to account for ion’s Coulomb interaction with its periodic >> images. > > > Sounds strange to me. I'd check the AMBER manual for what this is and how it > works (don't think you'll find anything) and then ask the authors of that > paper what they really mean. As Darden et al note (JCP 109 10921) at the end > of section IIB, the so-called "self term" and the "self potential" are > different things, and this is possibly a problem. > > Mark > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] itp file for D2O
Surya Prakash Tiwari On Tue, Dec 6, 2011 at 20:34, Justin A. Lemkul wrote: > > > Surya Prakash Tiwari wrote: >> >> Hi, >> >> I think you simply use #include "spce.itp" in your topology file. >> Please see http://www.gromacs.org/Documentation/Include_File_Mechanism >> > > This will not give D2O - the SPC/E water model is for H2O. I would suggest > to the OP to search for a suitable D2O model. I suspect there is one out > there. I meant that he usually uses #include "spce.itp" for SPC/E water model. Sorry abt the confusion. > > -Justin > >> Thanks. >> >> Surya Prakash Tiwari >> >> >> >> On Tue, Dec 6, 2011 at 19:53, cuong nguyen wrote: >>> >>> Dear GROMACS users, >>> >>> I usually use spce.itp file for water solvent in my simulation. However, >>> now >>> I want to change this solvent to deuterium monoxide (D2O). >>> >>> Please let me know if I have to change this itp file? if yes, where can I >>> find this file? >>> >>> Thank you very much. >>> >>> Best regards, >>> >>> >>> Nguyen Van Cuong >>> PhD student - Curtin University of Technology >>> Mobile: (+61) 452213981 >>> >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> Please don't post (un)subscribe requests to the list. Use the >>> www interface or send it to gmx-users-requ...@gromacs.org. >>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Re: [gmx-users] itp file for D2O
Hi, I think you simply use #include "spce.itp" in your topology file. Please see http://www.gromacs.org/Documentation/Include_File_Mechanism Thanks. Surya Prakash Tiwari On Tue, Dec 6, 2011 at 19:53, cuong nguyen wrote: > Dear GROMACS users, > > I usually use spce.itp file for water solvent in my simulation. However, now > I want to change this solvent to deuterium monoxide (D2O). > > Please let me know if I have to change this itp file? if yes, where can I > find this file? > > Thank you very much. > > Best regards, > > > Nguyen Van Cuong > PhD student - Curtin University of Technology > Mobile: (+61) 452213981 > > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Simulation of a charged system
Dear Gromacs users, I am simulating a charged system with periodic boundary conditions. My system has 506 water molecules and one ion. I am trying to calculate the free energy of an ion. I do not want to use any counter-ions to neutralize the system, because I don't have force-field between my ion and the counterion. In particular, I want to reproduce the following paper: Horinek, D., Mamatkulov, S. I., & Netz, R. R. (2009). Rational design of ion force fields based on thermodynamic solvation properties. The Journal of chemical physics, 130(12), 124507. doi:10.1063/1.3081142 Their system is also charged, has one ion and 506 water molecules. They are using AMBER software. On page number 7, they have discussed the correction terms due to ewald summation (equation 6) in a charaged system. On the same page, they further say that AMBER has implemented first term in eqn. 6 to account for ion’s Coulomb interaction with its periodic images: "In the PME implementation in AMBER, a self-energy correction of N*e^2 *xi /(8*pi*epsilon) is already accounted for." I just want to know whether, Gromacs has the same implementation in their PME to account for ion’s Coulomb interaction with its periodic images. Thanks in advance. Regards, Surya Prakash Tiwari -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
