----- Original Message ----- From: Fabrizio Marinelli <[email protected]> Date: Friday, April 30, 2010 19:17 Subject: [gmx-users] Problem in the gromacs git version To: [email protected], Discussion list for GROMACS users <[email protected]>
> Hi all, > i have downloaded and installed the latest gromacs git version > with the > purpose of testing the charmm force field. I noticed that with > pdb2gmx i > am able to construct the topology without problems and also to > run the > simulation. Then when i look to the energy terms i notice that SR > interaction are 0 and this of course generate problems to the > simulationeven if it does not crush. I also tried with the > GROMOS96 43a1 force field > and it gives the same. I also tried to remove the protein and > run only > water molecules and still SR are 0. I tried also to run the > simulation of > spc216.gro water box, and it still gives the same. > Does any one of you faced with the same problem? If not, could > some you > try the same test to see if you find the same? Could some of you > eventually propose a solution? I was using git master this week without observing such a problem. Two approaches to a solution occur to me. Either vary your .mdp entries until it works, which can identify the broken algorithm, or, use git to go back in time until you find a point where the simulation works. Then the erroneous commit, if any, can be found. What's best will depend why you're using the git version. Mark > > 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 -- 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
