It is maybe probably general (or in my mdp. file for example or in the code), i tryed with gromos43a1.ff and it gives the same: SR interaction are 0. Fabrizio
> > > Fabrizio Marinelli wrote: >> Here it is my .mdp file, i attach you also the topology file, just to be >> more specific the one that are 0 are the SR interactions, thank you very >> much. > > For diagnostic purposes, can you re-process your structure using a > different > force field and try again? If the energies are still coming up zero, then > there > may be something wrong in the code as a whole, otherwise it is specific to > the > CHARMM force field. Either way, I'm out of my league on this one :) > Maybe a > developer can comment. > > -Justin > >> Fabrizio >> >> title = Teaa MD >> cpp = /lib/cpp >> include = >> integrator = md >> comm_mode = Linear >> nstcomm = 10 >> tinit = 0 >> comm-grps = System >> dt = 0.002 >> nsteps = 6000000 >> ; OUTPUT CONTROL OPTIONS = >> ; Output frequency for coords (x), velocities (v) and forces (f) = >> nstxout = 5000 >> nstvout = 5000 >> ; Output frequency for energies to log file and energy file = >> nstlog = 500 >> nstenergy = 500 >> nstxtcout = 500 >> xtc-precision = 100000 >> xtc_grps = System >> energygrps = System >> pbc = xyz >> nstlist = 5 >> epsilon_r = 1. >> ns_type = grid >> coulombtype = pme >> vdwtype = Cut-Off >> fourierspacing = 0.12 >> ; EWALD/PME/PPPM parameters >> pme_order = 4 >> ewald_rtol = 2.2e-05 >> epsilon_surface = 0 >> optimize_fft = yes >> rlist = 1.2 >> rcoulomb = 1.2 >> rvdw = 1.2 >> tcoupl = Berendsen >> tc-grps = System >> tau_t = 1.0 >> ref_t = 298 >> pcoupl = Berendsen >> pcoupltype = isotropic >> tau_p = 2.5 >> compressibility = 4.5e-5 >> ref_p = 1.0 >> ; Dielectric constant of reaction field = >> epsilon_rf = 80.0 >> gen_vel = yes >> gen_temp = 298 >> gen_seed = 173529 >> constraints = all-bonds >> constraint_algorithm = lincs >> shake_tol = 0.0001 >> ; Highest order in the expansion of the constraint coupling matrix = >> lincs-order = 4 >> ; Lincs will write a warning to the stderr if in one step a bond = >> ; rotates over more degrees than = >> lincs-warnangle = 30 >> user1-grps = System >> ; Non-equilibrium MD stuff = >> acc-grps = >> accelerate = >> freezegrps = >> freezedim = >> cos-acceleration = >> >> >>> >>> Fabrizio Marinelli wrote: >>>> Hi all, >>>> I have downloaded the latest git version of gromacs (yesterday) in >>>> which >>>> it is possible to use the charmm27 force field, I constructed the >>>> topology >>>> for my protein using the pdb2gmx program, everything goes ok also with >>>> the >>>> solvation, but then when i run the MD i notice that coulomb and LJ >>>> interaction are 0 and also the protein consequently unfold. >>>> Did any of you found this kind of problem? Could some of you rpopose >>>> eventually a solution? >>> Can you post your .mdp file? >>> >>> -Justin >>> >>>> Thanks in advance, >>>> Fabrizio >>>> >>>> >>>> ---------------------------------------------------------------- >>>> SISSA Webmail https://webmail.sissa.it/ >>>> Powered by SquirrelMail http://www.squirrelmail.org/ >>>> >>> -- >>> ======================================== >>> >>> 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 [email protected] >>> 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 [email protected]. >>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >>> >> >> >> >> ---------------------------------------------------------------- >> SISSA Webmail https://webmail.sissa.it/ >> Powered by SquirrelMail http://www.squirrelmail.org/ > > -- > ======================================== > > 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 [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > ---------------------------------------------------------------- SISSA Webmail https://webmail.sissa.it/ Powered by SquirrelMail http://www.squirrelmail.org/ -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
