Thanks David for the response. I was going through the supporting material of your paper to understand the methodology . For G96 forcefield, you wrote 'For the gromos96 simulations marked “cutoff ” a reaction field with ǫ = 54 was applied beyond a cutoff of14 Å, for the opls/aa “cutoff ” simulations a straight cut-off of14 Å was chosen, and for the charmm “cutoff ” simulations a shift function was used between 10 and 12 Å. In addition, simulations were carried out using Particle Mesh Ewald (PME) for the calculation of electrostatic interactions[10, 11].'
I am wondering what does the statement ' marked cutoff a reaction field with epsilon 54 beyond a cutoff of 14 Angstrom' in terms of gromacs .mdp terminology ? Does it mean that you used reaction field as long range electrostatics for G96. But, I may have understood wrong because in the last line you again write, all simulations used 'PME'.. Does it mean that for G96 , the simulations were repeated with both reaction field and PME separately ? For the reaction field, I have never used it before, so I was wondering if you can provide bit more details in 'mdout.mdp' terminolgy for general setup of simulation using G96 forcefield . For example, for my simulation using Gromos96, I was using following mdout.mdp using PME. I am not sure that is a suitable setup for gromos simulation or not . Also, if I wanted to use reaction field, what modification I should have made here in long-range electrostat part ? ; RUN CONTROL PARAMETERS integrator = md ; Start time and timestep in ps tinit = 0.0 dt = 0.004 nsteps = 40000000 ; For exact run continuation or redoing part of a run init_step = 0 ; mode for center of mass motion removal comm-mode = Linear ; number of steps for center of mass motion removal nstcomm = 1 ; group(s) for center of mass motion removal comm-grps = ; NEIGHBORSEARCHING PARAMETERS ; nblist update frequency nstlist = 10 ; ns algorithm (simple or grid) ns_type = grid ; Periodic boundary conditions: xyz (default), no (vacuum) ; or full (infinite systems only) pbc = xyz ; nblist cut-off rlist = 1.4 domain-decomposition = no ; OPTIONS FOR ELECTROSTATICS AND VDW ; Method for doing electrostatics coulombtype = pme rcoulomb-switch = 0 rcoulomb = 1.4 ; Relative dielectric constant for the medium and the reaction field epsilon_r = 1 epsilon_rf = 1 ; Method for doing Van der Waals vdw-type = cut-off ; cut-off lengths ;rvdw-switch = 0.7 rvdw = 1.4 ; Apply long range dispersion corrections for Energy and Pressure DispCorr = no ; Extension of the potential lookup tables beyond the cut-off table-extension = 1 ; Seperate tables between energy group pairs energygrp_table = ; Spacing for the PME/PPPM FFT grid fourierspacing = 0.12 ; FFT grid size, when a value is 0 fourierspacing will be used fourier_nx = 0 fourier_ny = 0 fourier_nz = 0 ; EWALD/PME/PPPM parameters pme_order = 6 ewald_rtol = 1e-6 ewald_geometry = 3d epsilon_surface = 0 optimize_fft = no ________________________________ From: David van der Spoel <[email protected]> To: Discussion list for GROMACS users <[email protected]> Sent: Wed, December 22, 2010 2:31:35 PM Subject: Re: [gmx-users] PME or Reaction field suitable for Gromos forcefield ? On 2010-12-22 21.57, Sanku M wrote: > > > ------------------------------------------------------------------------ > *From:* Sanku M <[email protected]> > *To:* [email protected] > *Sent:* Wed, December 22, 2010 1:06:09 PM > *Subject:* PME of Reaction field for Gromos forcefield ? > > Hi, > I was trying to use g53a5 gromos forcefield for my study of protein in > water . But, I found the original parameterization paper of gromos , in > general uses reaction field for considering long range electrostatics . > But, I was wondering among PME and reaction field , which one will be > more apprpriate . Does PME cause any artifact if used with Gromos > forcefield ? > Alternatively, if I can get a sample .mdp file for typical gromos > forcefield simulation, that will also be very helpful . > Sanku > > > Check out Oliver Lange, David van der Spoel and Bert de Groot: Scrutinizing Molecular Mechanics Force Fields on the Microsecond Timescale With NMR Data Biophys. J. 99 pp. 647-655 (2010) We find that all FF perform better with PME. -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. [email protected] http://folding.bmc.uu.se -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
