Hi Justin, this atom is the CG atom of the phosphate I added to the protein. But how can I find out by what it is punished?
This is the topology for this residue in the aminoacid.rtp file. I added it manually. The parameter are from the amber parameter database (http://www.pharmacy.manchester.ac.uk/bryce/amber/): [ TYP ] [ atoms ] N N -0.516300 1 CA CT 0.275503 2 HA H1 0.008223 3 CB CT -0.354052 4 HB1 HC 0.110326 5 HB2 HC 0.110326 6 CG CA 0.119728 7 CD1 CA -0.198938 8 HD1 HA 0.137143 9 CE1 CA -0.284884 10 HE1 HA 0.177179 11 CZ C 0.452616 12 OH OS -0.534452 13 H H 0.293600 14 CE2 CA -0.284884 15 HE2 HA 0.177179 16 CD2 CA -0.198938 17 HD2 HA 0.137143 18 C C 0.536600 19 O O -0.581900 20 P P 1.393213 21 OP1 OH -0.752821 22 OP2 O2 -0.822464 23 OP3 O2 -0.822464 24 H1P HO 0.423316 25 [ bonds ] N H N CA CA HA CA CB CA C CB HB1 CB HB2 CB CG CG CD1 CG CD2 CD1 HD1 CD1 CE1 CE1 HE1 CE1 CZ CZ OS CZ CE2 OS P CE2 HE2 CE2 CD2 CD2 HD2 C O -C N P OP1 P OP2 P OP3 OP1 H1P [ impropers ] -C CA N H CA +N C O CG CE2 CD2 HD2 CZ CD2 CE2 HE2 CD1 CZ CE1 HE1 CG CE1 CD1 HD1 CD1 CD2 CG CB CE1 CE2 CZ OH Additionally I had to add an entry in the ffbonded file in the part [ dihedraltypes ] CA CA C OS 4 180.00 4.60240 2 ; Here I am not completely sure about the entry because I could not find a source for this combination of atoms. But there is already an entry for the combination CA CA C OH Which has the same parameters. Could this be the problem? And if it could be, can you please give me hint where I can find parameters for it? Because I really could not find it. Thank you, Eva > > > On 9/12/12 3:39 PM, reising...@rostlab.informatik.tu-muenchen.de wrote: >> Hi Justin, >> my mdp file for the md run looks like this: >> >> define = -DPOSRES >> integrator = md >> dt = 0.001 >> nsteps = 5000 >> nstxout = 100 >> nstvout = 0 >> nstfout = 0 >> nstlog = 1000 >> nstxtcout = 500 >> nstenergy = 5 >> energygrps = Protein Non-Protein >> nstcalcenergy = 5 >> nstlist = 10 >> ns-type = Grid >> pbc = xyz >> rlist = 0.9 >> coulombtype = PME >> rcoulomb = 0.9 >> rvdw = 0.9 >> fourierspacing = 0.12 >> pme_order = 4 >> ewald_rtol = 1e-5 >> gen_vel = yes >> gen_temp = 200.0 >> gen_seed = 9999 >> constraints = all-bonds >> tcoupl = V-rescale >> tc-grps = Protein System_&_!Protein >> tau_t = 0.1 0.1 >> ref_t = 298 298 >> pcoupl = no >> freezegrps = Protein_&_!TYP >> freezedim = Y Y Y >> >> >> I added a phosphate (TYP) to my protein and now want to do first a >> minimization (which I already did), then a short md run (for the case >> that >> I am in a local minima) and after that again a minimization. >> Since I only want to minimize the energy of the phosphate I freezed the >> rest of the protein (Protein_&_!TYP). >> >> >> Since on my cluster I am not allowed to run long jobs I had to divide >> the >> minimization run in several runs. The output of the last run was: >> >> Steepest Descents converged to machine precision in 15 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.7264606e+05 >> Maximum force = 1.6227990e+04 on atom 961 >> Norm of force = 1.2328220e+02 >> >> gcq#192: "It's So Fast It's Slow" (F. Black) >> >> >> Steepest Descents converged to machine precision in 15 steps, >> but did not reach the requested Fmax < 10. >> Potential Energy = -7.7264606e+05 >> Maximum force = 1.6227990e+04 on atom 961 >> Norm of force = 1.2328220e+02 >> >> >> After this minimization run I wanted to do the md run. >> >> My protein is a membrane protein with its surrounding membrane. I >> already >> did a minimization and md run with this protein but without the >> phosphate. >> The only difference to the time when everything worked fine is the >> phosphate. >> >> Does this help you somehow to see the failure? >> > > Your minimization is insufficient. You have a maximum force in excess of > 16000 > on atom 961. Such a large force explains the crash. You should > investigate > what this atom is and what is pushing on it so hard. > > -Justin > > -- > ======================================== > > Justin A. Lemkul, Ph.D. > Research Scientist > 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 gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
