[gmx-users] RE: RE: RE: Doubts over g_lie usage
Thank you so much for your time and explanation. I am recalculating the energy co-ordinates and using it in g_lie calculations. I have read the manual and changed the .mdp file I am using. The following is the mdp file, please check for the correctness. The text in bold font are newly included after your suggestions. Can I use this mdp to calculate the LIE correctly? cpp = /usr/bin/cpp constraints = all-bonds integrator = md dt = 0.002; ps ! nsteps = 500 ; total 1 ps. nstcomm = 1 nstxout = 5000 nstvout = 5000 nstfout = 0 nstlog = 5000 nstenergy = 500 nstxtcout = 500 nstlist = 10 ns_type = grid rlist = 1.2 ; short-range neighborlist cutoff (in nm) rcoulomb= 0.9 ; short-range electrostatic cutoff (in nm) vdwtype = cut-off rvdw= 1.4 ; gromos96 force field/ short-range van der Waals cutoff (in nm) ;coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics ;fourierspacing = 0.12; grid spacing for FFT ;fourier_nx = 0 ;fourier_ny = 0 ;fourier_nz = 0 ;pme_order = 4 ;ewald_rtol = 1e-5 *coulombtype = Reaction-Field-zero epsilon_rf = 0* optimize_fft= yes pbc = xyz ; modified Berendsen temperature coupling is on in two groups Tcoupl = V-rescale; modified Berendsen thermostat tc-grps = S04 SOL tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = S04 SOL ; Mode for center of mass motion removal comm-mode = Linear ; Groups for center of mass motion removal comm-grps = System ; Pressure coupling is now on Pcoupl = parrinello-rahman Pcoupltype = isotropic tau_p = 1.0 compressibility = 4.5e-5 ref_p = 1.0 ; Generate velocites is on at 300 K. gen_vel = yes gen_temp= 300.0 gen_seed= 173529 ~ Thanks Peterson J -- View this message in context: http://gromacs.5086.n6.nabble.com/Doubts-over-g-lie-usage-tp5000130p5000244.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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] RE: RE: RE: Doubts over g_lie usage
There are different methods used to calculate the electrostatics, RF-0 is one. 7.3.10 in the manual. You can just use the -rerun flag in mdrun, after creating an appropriate .tpr file with grompp and a new .mdp file. If I understand it properly this effectively calculates single point interaction energies for each frame in your trajectory that you save co-ordinates for, so it is much, much, faster than redoing the calculations. Have fun, Tom Thanks for that explanation. I would like to know this with little more detail. What do you mean by RF-0 and which cut-off value are you talking about? Rerunning the trajectory means the whole MD run again? Thanks. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * 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
