Justin, with that charmm27 cutoffs (rlist=1.2 rlistlong=1.4 rcoulomb=1.2 rvdw=1.2 rvdw_switch=0.8 and vdwtype=switch) I've obtain 2 notes from grompp
NOTE 1 [file ./mdps/em.mdp]: For energy conservation with switch/shift potentials, rlist should be 0.1 to 0.3 nm larger than rvdw. NOTE 2 [file ./mdps/em.mdp]: The sum of the two largest charge group radii (0.078024) is larger than rlist (1.200000) - rvdw (1.200000) Should I increase Rlist to the 1.4 ( as well as rcoulomb to the same value because of PME) ? 2012/12/7, Justin Lemkul <jalem...@vt.edu>: > > > On 12/7/12 1:19 PM, James Starlight wrote: >> Justin, >> >> following to your advise I've tried to use charmm 27 ff for simulation >> of my protein-cGMP complex ( ligand was parametrized by Swiss Param >> server). >> >> Could you provide me with the cut-offs for vdw as well as >> electrostatics suitable for simulation in charmm27 and 36 force >> fields? >> > > http://lists.gromacs.org/pipermail/gmx-users/2012-September/074717.html > >> Does anybody know another servers for parametrization of the ligands >> for charmm simulation in gromacs? >> > > If Google can't find it, it probably doesn't exist. > > -Justin > >> 2012/12/7, Justin Lemkul <jalem...@vt.edu>: >>> >>> >>> On 12/7/12 11:42 AM, James Starlight wrote: >>>> Justin, >>>> >>>> ligand-only simulation in vacuum have been finished with the same >>>> errors >>>> :) >>>> >>>> Step 19200, time 38.4 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 0.025443, max 0.140660 (between atoms 1 and 3) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 1 2 52.2 0.1033 0.0985 0.1000 >>>> 1 3 90.1 0.1168 0.1141 0.1000 >>>> >>>> Step 19200, time 38.4 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 0.025376, max 0.140474 (between atoms 1 and 3) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 1 2 52.0 0.1033 0.0988 0.1000 >>>> 1 3 90.0 0.1168 0.1140 0.1000 >>>> step 19200, will finish Sat Dec 8 04:10:49 2012 >>>> Step 19201, time 38.402 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 0.052715, max 0.293316 (between atoms 1 and 3) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 1 2 49.3 0.0988 0.0993 0.1000 >>>> 1 3 90.0 0.1140 0.1293 0.1000 >>>> >>>> Step 19201, time 38.402 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 0.052900, max 0.294281 (between atoms 1 and 3) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 1 2 49.6 0.0988 0.0989 0.1000 >>>> 1 3 90.0 0.1140 0.1294 0.1000 >>>> >>>> Step 19202, time 38.404 (ps) LINCS WARNING >>>> relative constraint deviation after LINCS: >>>> rms 0.035783, max 0.198482 (between atoms 1 and 3) >>>> bonds that rotated more than 30 degrees: >>>> atom 1 atom 2 angle previous, current, constraint length >>>> 1 2 33.3 0.0989 0.0984 0.1000 >>>> 1 3 89.9 0.1294 0.1198 0.1000 >>>> >>>> ------------------------------------------------------- >>>> Program mdrun, VERSION 4.5.4 >>>> Source code file: /tmp/gromacs-4.5.4/src/mdlib/constr.c, line: 176 >>>> >>>> Fatal error: >>>> Too many LINCS warnings (1000) >>>> >>>> >>>> ITs intresting that the same files (like step-1c_n11.pdb) have been >>>> produced already during CG minimisation phase but the system have not >>>> been crashed. So I suppoe that the problem is in geometry of the >>> >>> If you get errors in the minimization, that should indicate that either >>> the >>> >>> topology or configuration is flawed. >>> >>>> mollecule. The direct comparison of the bonds and angles with the rtp >>>> (DGUA) is non trivial again because of differs in the file formats >>>> representation :) >>>> >>> >>> Most troubleshooting is not easy. You can also create a topology for >>> DGUA >>> from >>> just about any DNA structure and compare its .top against your cGMP >>> topology. >>> >>> -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 >>> > > -- > ======================================== > > 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? 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