<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Fabrizio,<div><br></div><div>Could you send me the input files and I'll take a look at it. You can send it to <a href="mailto:bjelkmar@cbr.su.se">bjelkmar@cbr.su.se</a></div><div><br></div><div>Regards,</div><div>Pär Bjelkmar</div><div><br><div><div>29 apr 2010 kl. 16.34 skrev <a href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>:</div><br class="Apple-interchange-newline"><blockquote type="cite"><span class="Apple-style-span" style="border-collapse: separate; font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">Message: 3<br>Date: Thu, 29 Apr 2010 10:33:53 -0400<br>From: "Justin A. Lemkul" <<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>Subject: Re: [gmx-users] Problem with Charmm in gromacs<br>To: "Gromacs Users' List" <<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>Message-ID: <<a href="mailto:4BD998D1.6010405@vt.edu">4BD998D1.6010405@vt.edu</a>><br>Content-Type: text/plain; charset=ISO-8859-1; format=flowed<br><br><br><br>Fabrizio Marinelli wrote:<br><blockquote type="cite">Here it is my .mdp file, i attach you also the topology file, just to be<br></blockquote><blockquote type="cite">more specific the one that are 0 are the SR interactions, thank you very<br></blockquote><blockquote type="cite">much.<br></blockquote><br>For diagnostic purposes, can you re-process your structure using a different<span class="Apple-converted-space"> </span><br>force field and try again? If the energies are still coming up zero, then there<span class="Apple-converted-space"> </span><br>may be something wrong in the code as a whole, otherwise it is specific to the<span class="Apple-converted-space"> </span><br>CHARMM force field. Either way, I'm out of my league on this one :) Maybe a<span class="Apple-converted-space"> </span><br>developer can comment.<br><br>-Justin<br><br><blockquote type="cite">Fabrizio<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">title = Teaa MD<br></blockquote><blockquote type="cite">cpp = /lib/cpp<br></blockquote><blockquote type="cite">include =<br></blockquote><blockquote type="cite">integrator = md<br></blockquote><blockquote type="cite">comm_mode = Linear<br></blockquote><blockquote type="cite">nstcomm = 10<br></blockquote><blockquote type="cite">tinit = 0<br></blockquote><blockquote type="cite">comm-grps = System<br></blockquote><blockquote type="cite">dt = 0.002<br></blockquote><blockquote type="cite">nsteps = 6000000<br></blockquote><blockquote type="cite">; OUTPUT CONTROL OPTIONS =<br></blockquote><blockquote type="cite">; Output frequency for coords (x), velocities (v) and forces (f) =<br></blockquote><blockquote type="cite">nstxout = 5000<br></blockquote><blockquote type="cite">nstvout = 5000<br></blockquote><blockquote type="cite">; Output frequency for energies to log file and energy file =<br></blockquote><blockquote type="cite">nstlog = 500<br></blockquote><blockquote type="cite">nstenergy = 500<br></blockquote><blockquote type="cite">nstxtcout = 500<br></blockquote><blockquote type="cite">xtc-precision = 100000<br></blockquote><blockquote type="cite">xtc_grps = System<br></blockquote><blockquote type="cite">energygrps = System<br></blockquote><blockquote type="cite">pbc = xyz<br></blockquote><blockquote type="cite">nstlist = 5<br></blockquote><blockquote type="cite">epsilon_r = 1.<br></blockquote><blockquote type="cite">ns_type = grid<br></blockquote><blockquote type="cite">coulombtype = pme<br></blockquote><blockquote type="cite">vdwtype = Cut-Off<br></blockquote><blockquote type="cite">fourierspacing = 0.12<br></blockquote><blockquote type="cite">; EWALD/PME/PPPM parameters<br></blockquote><blockquote type="cite">pme_order = 4<br></blockquote><blockquote type="cite">ewald_rtol = 2.2e-05<br></blockquote><blockquote type="cite">epsilon_surface = 0<br></blockquote><blockquote type="cite">optimize_fft = yes<br></blockquote><blockquote type="cite">rlist = 1.2<br></blockquote><blockquote type="cite">rcoulomb = 1.2<br></blockquote><blockquote type="cite">rvdw = 1.2<br></blockquote><blockquote type="cite">tcoupl = Berendsen<br></blockquote><blockquote type="cite">tc-grps = System<br></blockquote><blockquote type="cite">tau_t = 1.0<br></blockquote><blockquote type="cite">ref_t = 298<br></blockquote><blockquote type="cite">pcoupl = Berendsen<br></blockquote><blockquote type="cite">pcoupltype = isotropic<br></blockquote><blockquote type="cite">tau_p = 2.5<br></blockquote><blockquote type="cite">compressibility = 4.5e-5<br></blockquote><blockquote type="cite">ref_p = 1.0<br></blockquote><blockquote type="cite">; Dielectric constant of reaction field =<br></blockquote><blockquote type="cite">epsilon_rf = 80.0<br></blockquote><blockquote type="cite">gen_vel = yes<br></blockquote><blockquote type="cite">gen_temp = 298<br></blockquote><blockquote type="cite">gen_seed = 173529<br></blockquote><blockquote type="cite">constraints = all-bonds<br></blockquote><blockquote type="cite">constraint_algorithm = lincs<br></blockquote><blockquote type="cite">shake_tol = 0.0001<br></blockquote><blockquote type="cite">; Highest order in the expansion of the constraint coupling matrix =<br></blockquote><blockquote type="cite">lincs-order = 4<br></blockquote><blockquote type="cite">; Lincs will write a warning to the stderr if in one step a bond =<br></blockquote><blockquote type="cite">; rotates over more degrees than =<br></blockquote><blockquote type="cite">lincs-warnangle = 30<br></blockquote><blockquote type="cite">user1-grps = System<br></blockquote><blockquote type="cite">; Non-equilibrium MD stuff =<br></blockquote><blockquote type="cite">acc-grps =<br></blockquote><blockquote type="cite">accelerate =<br></blockquote><blockquote type="cite">freezegrps =<br></blockquote><blockquote type="cite">freezedim =<br></blockquote><blockquote type="cite">cos-acceleration =<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Fabrizio Marinelli wrote:<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Hi all,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">I have downloaded the latest git version of gromacs (yesterday) in which<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">it is possible to use the charmm27 force field, I constructed the<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">topology<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">for my protein using the pdb2gmx program, everything goes ok also with<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">solvation, but then when i run the MD i notice that coulomb and LJ<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">interaction are 0 and also the protein consequently unfold.<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Did any of you found this kind of problem? Could some of you rpopose<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">eventually a solution?<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Can you post your .mdp file?<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">-Justin<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Thanks in advance,<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">Fabrizio<br></blockquote></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br class="Apple-interchange-newline"></blockquote></blockquote></span></blockquote></div><br></div></body></html>