Hi, bugs should be reported to bugzilla.gromacs.org. This way they are not forgotten.
Roland On Fri, Apr 30, 2010 at 7:12 AM, Fabrizio Marinelli <[email protected]>wrote: > Hi all, i have found the source of the error. I was compiling the latest > gromacs git version using the option --enable-fortran during the > configuration, this for the system i used (even the simple 216 spc box) > and for a generic force field gives SR interactions = 0. > Eliminating the option --enable-fortran everything works and the energies > are the same of gromacs-4.0.5. > This maybe useful for some of you. > Best, > Fabrizio > > > > > > > ----- 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 > > > > > > ---------------------------------------------------------------- > 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 > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309
-- 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
