Hi,<div><br></div><div>bugs should be reported to <a href="http://bugzilla.gromacs.org">bugzilla.gromacs.org</a>. This way they are not forgotten.</div><div><br></div><div>Roland<br><br><div class="gmail_quote">On Fri, Apr 30, 2010 at 7:12 AM, Fabrizio Marinelli <span dir="ltr"><<a href="mailto:marinell@sissa.it">marinell@sissa.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi all, i have found the source of the error. I was compiling the latest<br>
gromacs git version using the option --enable-fortran during the<br>
configuration, this for the system i used (even the simple 216 spc box)<br>
and for a generic force field gives SR interactions = 0.<br>
Eliminating the option --enable-fortran everything works and the energies<br>
are the same of gromacs-4.0.5.<br>
This maybe useful for some of you.<br>
Best,<br>
Fabrizio<br>
<br>
><br>
><br>
> ----- Original Message -----<br>
> From: Fabrizio Marinelli <<a href="mailto:marinell@sissa.it">marinell@sissa.it</a>><br>
> Date: Friday, April 30, 2010 19:17<br>
> Subject: [gmx-users] Problem in the gromacs git version<br>
> To: <a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>, Discussion list for GROMACS users<br>
> <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>
><br>
>> Hi all,<br>
>> i have downloaded and installed the latest gromacs git version<br>
>> with the<br>
>> purpose of testing the charmm force field. I noticed that with<br>
>> pdb2gmx i<br>
>> am able to construct the topology without problems and also to<br>
>> run the<br>
>> simulation. Then when i look to the energy terms i notice that SR<br>
>> interaction are 0 and this of course generate problems to the<br>
>> simulationeven if it does not crush. I also tried with the<br>
>> GROMOS96 43a1 force field<br>
>> and it gives the same. I also tried to remove the protein and<br>
>> run only<br>
>> water molecules and still SR are 0. I tried also to run the<br>
>> simulation of<br>
>> spc216.gro water box, and it still gives the same.<br>
>> Does any one of you faced with the same problem? If not, could<br>
>> some you<br>
>> try the same test to see if you find the same? Could some of you<br>
>> eventually propose a solution?<br>
><br>
> I was using git master this week without observing such a problem.<br>
><br>
> Two approaches to a solution occur to me. Either vary your .mdp entries<br>
> until it works, which can identify the broken algorithm, or, use git to go<br>
> back in time until you find a point where the simulation works. Then the<br>
> erroneous commit, if any, can be found.<br>
><br>
> What's best will depend why you're using the git version.<br>
><br>
> Mark<br>
><br>
>> > Fabrizio Marinelli wrote:<br>
>> >> Here it is my .mdp file, i attach you also the topology file,<br>
>> just to be<br>
>> >> more specific the one that are 0 are the SR interactions,<br>
>> thank you very<br>
>> >> much.<br>
>> ><br>
>> > For diagnostic purposes, can you re-process your structure<br>
>> using a<br>
>> > different<br>
>> > force field and try again? If the energies are still<br>
>> coming up zero, then<br>
>> > there<br>
>> > may be something wrong in the code as a whole, otherwise it is<br>
>> specific to<br>
>> > the<br>
>> > CHARMM force field. Either way, I'm out of my league on<br>
>> this one :)<br>
>> > Maybe a<br>
>> > developer can comment.<br>
>> ><br>
>> > -Justin<br>
>> ><br>
>> >> Fabrizio<br>
>> >><br>
>> >><br>
>> title = Teaa MD<br>
>> >><br>
>> cpp = /lib/cpp<br>
>> >><br>
>> include =<br>
>> >><br>
>> integrator = md<br>
>> >><br>
>> comm_mode = Linear<br>
>> >><br>
>> nstcomm = 10<br>
>> >><br>
>> tinit = 0<br>
>> >> comm-<br>
>> grps = System<br>
>> >><br>
>> dt = 0.002<br>
>> >><br>
>> nsteps = 6000000<br>
>> >> ; OUTPUT CONTROL OPTIONS =<br>
>> >> ; Output frequency for coords (x), velocities (v) and forces<br>
>> (f) =<br>
>> >><br>
>> nstxout = 5000<br>
>> >><br>
>> nstvout = 5000<br>
>> >> ; Output frequency for energies to log file and energy file =<br>
>> >><br>
>> nstlog = 500<br>
>> >><br>
>> nstenergy = 500<br>
>> >><br>
>> nstxtcout = 500<br>
>> >> xtc-<br>
>> precision = 100000<br>
>> >><br>
>> xtc_grps = System<br>
>> >><br>
>> energygrps = System<br>
>> >><br>
>> pbc = xyz<br>
>> >><br>
>> nstlist = 5<br>
>> >><br>
>> epsilon_r = 1.<br>
>> >><br>
>> ns_type = grid<br>
>> >><br>
>> coulombtype = pme<br>
>> >><br>
>> vdwtype = Cut-Off<br>
>> >><br>
>> fourierspacing = 0.12<br>
>> >> ; EWALD/PME/PPPM parameters<br>
>> >><br>
>> pme_order = 4<br>
>> >><br>
>> ewald_rtol = 2.2e-05<br>
>> >><br>
>> epsilon_surface = 0<br>
>> >><br>
>> optimize_fft = yes<br>
>> >><br>
>> rlist = 1.2<br>
>> >><br>
>> rcoulomb = 1.2<br>
>> >><br>
>> rvdw = 1.2<br>
>> >><br>
>> tcoupl = Berendsen<br>
>> >> tc-<br>
>> grps = System<br>
>> >><br>
>> tau_t = 1.0<br>
>> >><br>
>> ref_t = 298<br>
>> >><br>
>> pcoupl = Berendsen<br>
>> >><br>
>> pcoupltype = isotropic<br>
>> >><br>
>> tau_p = 2.5<br>
>> >><br>
>> compressibility = 4.5e-5<br>
>> >><br>
>> ref_p = 1.0<br>
>> >> ; Dielectric constant of reaction field =<br>
>> >><br>
>> epsilon_rf = 80.0<br>
>> >><br>
>> gen_vel = yes<br>
>> >><br>
>> gen_temp = 298<br>
>> >><br>
>> gen_seed = 173529<br>
>> >><br>
>> constraints = all-bonds<br>
>> >> constraint_algorithm = lincs<br>
>> >><br>
>> shake_tol = 0.0001<br>
>> >> ; Highest order in the expansion of the constraint coupling<br>
>> matrix =<br>
>> >> lincs-<br>
>> order = 4<br>
>> >> ; Lincs will write a warning to the stderr if in one step a<br>
>> bond =<br>
>> >> ; rotates over more degrees than =<br>
>> >> lincs-<br>
>> warnangle = 30<br>
>> >> user1-<br>
>> grps = System<br>
>> >> ; Non-equilibrium MD stuff =<br>
>> >> acc-<br>
>> grps =<br>
>> >><br>
>> accelerate =<br>
>> >><br>
>> freezegrps =<br>
>> >><br>
>> freezedim =<br>
>> >> cos-<br>
>> acceleration =<br>
>> >><br>
>> >><br>
>> >>><br>
>> >>> Fabrizio Marinelli wrote:<br>
>> >>>> Hi all,<br>
>> >>>> I have downloaded the latest git version of gromacs<br>
>> (yesterday) in<br>
>> >>>> which<br>
>> >>>> it is possible to use the charmm27 force field, I<br>
>> constructed the<br>
>> >>>> topology<br>
>> >>>> for my protein using the pdb2gmx program, everything goes<br>
>> ok also with<br>
>> >>>> the<br>
>> >>>> solvation, but then when i run the MD i notice that coulomb<br>
>> and LJ<br>
>> >>>> interaction are 0 and also the protein consequently unfold.<br>
>> >>>> Did any of you found this kind of problem? Could some of<br>
>> you rpopose<br>
>> >>>> eventually a solution?<br>
>> >>> Can you post your .mdp file?<br>
>> >>><br>
>> >>> -Justin<br>
>> >>><br>
>> >>>> Thanks in advance,<br>
>> >>>> Fabrizio<br>
>> >>>><br>
>> >>>><br>
>> >>>> ------------------------------------------------------------<br>
>> ----<br>
>> >>>> SISSA Webmail <a href="https://webmail.sissa.it/" target="_blank">https://webmail.sissa.it/</a><br>
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>> >>>><br>
>> >>> --<br>
>> >>> ========================================<br>
>> >>><br>
>> >>> Justin A. Lemkul<br>
>> >>> Ph.D. Candidate<br>
>> >>> ICTAS Doctoral Scholar<br>
>> >>> MILES-IGERT Trainee<br>
>> >>> Department of Biochemistry<br>
>> >>> Virginia Tech<br>
>> >>> Blacksburg, VA<br>
>> >>> jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>> >>> <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>> >>><br>
>> >>> ========================================<br>
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>> >><br>
>> >><br>
>> >><br>
>> >> --------------------------------------------------------------<br>
>> --<br>
>> >> SISSA Webmail <a href="https://webmail.sissa.it/" target="_blank">https://webmail.sissa.it/</a><br>
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>> ><br>
>> > --<br>
>> > ========================================<br>
>> ><br>
>> > Justin A. Lemkul<br>
>> > Ph.D. Candidate<br>
>> > ICTAS Doctoral Scholar<br>
>> > MILES-IGERT Trainee<br>
>> > Department of Biochemistry<br>
>> > Virginia Tech<br>
>> > Blacksburg, VA<br>
>> > jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
>> > <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
>> ><br>
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