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? 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