Dear GROMACS developers and users, I observed a problem with energy conservation in NVE simulation with nonbond potential lookup table. I use the same setup for the L-J particles, one in the "analytical" way in the *.itp file as functional form 1 (with vdw_type= switch), the other using User define table provided in /share/gromacs/top/table6-12.xvg (with vdw_type=User).
For unknown reason(s), the "analytical" one attains fairly good energy conservation, while the lookup table one doesn't (even after I changed the spacing interval from 0.002 nm to 0.001 nm). Is it a bug or a silly mistake I made? I have been checking it for the whole day, search through the manual and mailing list and I just cannot find anything particularly helpful. I am using GROMACS 4.0.5 and I use 3.3.3 (change the table and the mdp file of accordingly of course) to make a test and the energy still doesn't conserve with table. But I am use the single precision for Gromacs executable and haven't check the double precision yet. Did anybody observe a similar problem before? While using potential lookup table, will it still have shift scheme or switch scheme? Any idea or suggestion will be really appreciated! Thank you in advanced for your help. Below are the details for the simulation (in GMX 4.0.5): 4 core, red hat, for 1ns NVE simulation; relevant lines in itp file from MARTINI (for both "analytical" and table case): ------------------------------------------------------------------------------------------ [ nonbond_params ] P1 P1 1 0.19402E-00 0.20914E-02 ; almost attractive ; test ;[ moleculetype ] ; molname nrexcl ;SOL 2 ;[ atoms ] ; nr type resnr residue atom cgnr charge mass ; 1 P1 1 SOL OW 1 0.0 -------------------------------------------------------------------------------------- mdp file for the "analytical" one, for the relevant lines: ---------------------------------------------------------------------- ; VARIOUS PREPROCESSING OPTIONS = title = Martini cpp = /usr/bin/cpp ; RUN CONTROL PARAMETERS = integrator = md ; start time and timestep in ps = tinit = 0.0 dt = 0.005 ; I am using a CG model nsteps = 200000 ; number of steps for center of mass motion removal = nstcomm = 1 ; NEIGHBORSEARCHING PARAMETERS = ; nblist update frequency = nstlist = 10 ; ns algorithm (simple or grid) = ns_type = grid ; Periodic boundary conditions: xyz or none = pbc = xyz ; nblist cut-off = rlist = 1.8 ; try to make the cut-off long enough ; OPTIONS FOR ELECTROSTATICS AND VDW = ; Method for doing electrostatics = coulombtype = shift ; no electrostatic in the system ;fourierspacing = 0.2 rcoulomb_switch = 0.0 ;pme_order = 6 rcoulomb = 1.6 ; Dielectric constant (DC) for cut-off or DC of reaction field = epsilon_r = 1.4 ; Method for doing Van der Waals = vdw_type = switch ; can still attain reasonable energy conservation ; cut-off lengths = rvdw_switch = 1.2 rvdw = 1.6 ; Apply long range dispersion corrections for Energy and Pressure = DispCorr = No ; NVE simulation ; OPTIONS FOR WEAK COUPLING ALGORITHMS = ; Temperature coupling = tcoupl = no ; Groups to couple separately = tc-grps = System ; Time constant (ps) and reference temperature (K) = tau_t = 0.05 ref_t = 300 ; Pressure coupling = Pcoupl = no Pcoupltype = semiisotropic ; Time constant (ps), compressibility (1/bar) and reference P (bar) = tau_p = 0.2 0.2 compressibility = 3e-5 3e-5 ref_p = 1.0 1.0 ; GENERATE VELOCITIES FOR STARTUP RUN = gen_vel = no gen_temp = 105 gen_seed = 473529 ------------------------------------------------------------------------------------------ results from g_energy for "analytical" one: ------------------------------------------------------------------------------------------ Energy Aver. RMSD Drift Potential -25618.5 150.676 0.00821594 Total Energy -16529 0.976822 0.000626028 ------------------------------------------------------------------------------------------ mdp file for the one using table. All lines are the same except the following two: ------------------------------------------------------------------------------------------ table-extension = 1.2 ; nm vdw_type = User -------------------------------------------------------------------------------------- The table is taken from the package 4.0.5 in /share/gromacs/top/table6-12.xvg. results from g_energy for "analytical" one: ------------------------------------------------------------------------------------------ Energy Aver. RMSD Drift Potential -30257.3 1516.79 -5.79857 Total Energy -25641 3017.7 -11.5046 ------------------------------------------------------------------------------------------ -- 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/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/mailing_lists/users.php
