1] My simulations in the production MD are for 10 ns. I am first doing energy minimization, followed by NPT run of 2ns (1000000; 0.002 * 1000000 = 2000 ps[2ns]), and then followed by NPT Production MD run for 10 ns (10000000; 0.001 * 10000000 = 10000 ps [10 ns]). During the npt simulation, the box length is reducing, and further during the nptmd ie., production md too the box length is getting reduced still further. I am not getting any idea over this... Is the time duration enough or still i need to do it for more timestep..??
2] Regarding the commands i use to get the mixtures into the simulation box are:- (a) creating the box:- gmx editconf -f abc.gro -o abcbox.gro -c -b X X X (b) inserting the molecules:- gmx insert-molecules -f abcbox.gro -ci def.gro -nmol X -o ghi.gro (c) Solvating the mixture with water :- gmx solvate -cp ghi.gro -cs spc216.gro -o jkl.gro -maxsol XXX So these are the commands which i give in order to generate my Simulation box containing Amino acid, TMAO and Water mixture. Hope these are the right set of commands... and then i start simulation...EM followed by NPT followed by NPTMD... Thank you... With Best Regards, DILIP.H.N Ph.D Student <https://mailtrack.io/> Sent with Mailtrack <https://mailtrack.io/install?source=signature&lang=en&referral=cy16f01.di...@nitk.edu.in&idSignature=22> <#> With Best Regards, DILIP.H.N Ph.D Student -- 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.