> >> Hello Gromacs users, >> >> I am trying to run MD simulation of chloroform in hydrated POPC in >> CHARMM36 ff. I did not observe anything wrong with the bond structure of >> chloroform after insert molecules or solvation. But after EM, when I looked >> em.gro in VMD, there were Cl-Cl bonds or Cl-H bonds formed on some >> chloroform molecules, which had not been there for npt.gro. I assume I need >> to use SHAKE to constrain those bonds during EM, but no completely sure. >> >> And I also want check if my "Adding a residue to a force field" process is >> done correctly. The following is what I did. >> >> ======================================================================== >> The chloroform atomtypes CCM HCM and CLCM are not included in the ff, so I >> first added them to the atomtypes.atp as >> CLCM 35.45000 ; >> HCM 1.00800 ; >> CCM 12.01100 ; >> >> Second, I added LJ parameters to ffnonbonded.itp as >> ;type atnum mass charge ptype sigma epsilon >> CLCM 17 35.450000 0.000 A 0.172067736185 1.25520 >> CCM 6 12.011000 0.000 A 0.170071301248 0.42677 >> HCM 1 1.008000 0.000 A 0.110044563280 0.08368 >> >> Third, I added bond info to ffbonded.itp as >> [ bondtypes ] >> ; i j func b0 kb >> CCM CLCM 1 0.17580000 418400.00 >> CCM HCM 1 0.11000000 418400.00 >> >> [ angletypes ] >> ; i j k func theta0 ktheta ub0 >> kub >> CLCM CCM CLCM 5 111.300000 0.000000 0.00000000 >> 0.00 >> HCM CCM CLCM 5 107.570000 0.000000 0.00000000 >> 0.00 >> >> Last, I added the following to the merged.rtp as >> [ chlo ] >> [ atoms ] >> C CCM 0.179 0 >> CL1 CLCM -0.087 1 >> CL2 CLCM -0.087 2 >> CL3 CLCM -0.087 3 >> HX HCM 0.082 4 >> >> [ bonds ] >> C CL1 >> C HX >> C CL2 >> C CL3 >> ======================================================================== >> The result from EM was >> Steepest Descents converged to Fmax < 500 in 5462 steps >> Potential Energy = -1.8603069e+05 >> Maximum force = 4.8871869e+02 on atom 18043 >> Norm of force = 1.0274749e+01
I would also change the etmol in your em.mdp file to 10 instead of 500. This should give you a better system before you pass it to NVT/NPT. Shi >> >> atom 18043 is the carbon of the chloroform that has weird Cl-Cl bond >> connected visually in VMD. >> >> >> Could anyone point out where I did wrong ? Thank you in advance. >> >> Lili Zhang >> -- >> Gromacs Users mailing list >> >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before >> posting! >> >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> * For (un)subscribe requests visit >> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or >> send a mail to gmx-users-requ...@gromacs.org. >> > > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
