Sent from Yahoo Mail on Android ----- Forwarded Message ----- From: "Afsane Farhadi" <afsane_farh...@yahoo.com> To: "gromacs.org_gmx-users@maillist.sys.kth.se" <gromacs.org_gmx-users@maillist.sys.kth.se> Cc: Sent: Mon, Apr 27, 2020 at 3:52 PM Subject: lincs warning Hi users I have two types of molecules ,methane and carbondioxide. i optimized them by gaussian calculation and i edited the atom name and residue by vim. I extracted the epsilon and sigma parameter from the articles . i generated a box of 500 methane molecules and 62 carbondioxide by insert-molecules. I have done energy minimization and its ok (potential energy is -2e+03).when i was running npt.mdp the lincs warning was showed( bond rotate more than 30 degree)I need help thanks alot for your quick answers .the topology and npt.mdp is:#include "oplsaa.ff/forcefield.itp"
[ atomtypes ] CO C01 12.0110 0.775 A 2.75700E-01 2.33790E-01 OC O01 15.99940 -0.388 A 3.03300E-01 6.69120E-01 opls_801 H801 1.0080 0.125 A 1.48720E-01 0.65688E-01 opls_803 H803 1.0080 0.125 A 1.48720E-01 0.65688E-01 opls_804 H804 1.0080 0.125 A 1.48720E-01 0.65688E-01 opls_800 C800 12.0110 -0.502 A 1.90820E-01 4.57729E-01 opls_802 H802 1.0080 0.125 A 1.48720E-01 0.65688E-01 [ moleculetype ] ; Name nrexcl CH4 3 [ atoms ] ; nr type resnr residue atom cgnr charge mass 1 opls_800 1 H C 1 -0.5020 12.0110 2 opls_801 1 H H 1 0.1250 1.0080 3 opls_802 1 H H 1 0.1250 1.0080 4 opls_803 1 H H 1 0.1250 1.0080 5 opls_804 1 H H 1 0.1250 1.0080 [ bonds ] 2 1 1 0.1090 138490.400 3 1 1 0.1090 138490.400 4 1 1 0.1090 138490.400 5 1 1 0.1090 138490.400 [ angles ] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 109.500 146.440 2 1 4 1 109.500 146.440 2 1 5 1 109.500 146.440 3 1 4 1 109.500 146.440 4 1 5 1 109.500 146.440 3 1 5 1 109.500 146.440 [ moleculetype ] ; Name nrexcl CAR 3 [atoms] ; nr type resnr residue atom cgnr charge mass 1 CO 1 CAR CO 1 0.775 12.0110 2 OC 1 CAR OC 1 -0.388 15.9994 3 OC 1 CAR OC 1 -0.388 15.9994 [ bonds ] 1 2 1 0.11620 844300 1 3 1 0.11620 844300 [angles] ; ai aj ak funct c0 c1 c2 c3 2 1 3 1 180 451.9 [system]: co2 in methane [molecules] CH4 500 CAR 62################ Sent from Yahoo Mail on Android -- 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.