On Fri, May 18, 2012 at 12:38 PM, Javier Cerezo <[email protected]> wrote: > Hi Steven > > You've tried with "constraints = none", but that still keeps constraints > over water molecules through SETTLE algorithm. Maybe you can try a > minimization with "define = -DFLEXIBLE" to remove settle over water and > then try again a constraint (settle) minimization. > > Javier >
Awesome! Thank you Javier, that really helped!!!! Steven > > El 18/05/12 12:58, Steven Neumann escribió: > > Dear Gmx Users, > > My system consists of a Tube made of Oxygen, Hydrogen and ions. These > atoms are not connected via bonds. I try tu run EM: > > ; minim.mdp - used as input into grompp to generate em.tpr > ; Parameters describing what to do, when to stop and what to save > > integrator = steep ; Algorithm (steep = steepest descent > minimization) > emtol = 1000.0 ; Stop minimization when the maximum force < > 1000.0 kJ/mol/nm > emstep = 0.001 > nsteps = 50000 ; Maximum number of (minimization) steps to > perform > nstxout = 1 > ; Parameters describing how to find the neighbors of each atom and how to > calculate the interactions > nstlist = 1 ; Frequency to update the neighbor list and long > range forces > ns_type = grid ; Method to determine neighbor list (simple, grid) > rlist = 1.4 ; Cut-off for making neighbor list (short range > forces) > coulombtype = PME ; Treatment of long range electrostatic > interactions > rcoulomb = 1.4 ; Short-range electrostatic cut-off > rvdw = 1.4 ; Short-range Van der Waals cut-off > pbc = xyz ; Periodic Boundary Conditions (yes/no) > > freezegrps = TUB > freezedim = Y Y Y > > > Then a lot of errors "water molecule on atom X cannot be settled". I tried: > > 1. constraints = none > > 2. remove those water molecules - then other water molecules have the same > error > > 3. using nstxout =1 in VMD, I could observe that some of the molecules > facing this error split in one frame (hydrogens 7A away from oxygen) or > spin around 180 degrees - it depends. > > 4. I tried increase vdwradii of the atoms which form my Tube so they wont > overlap with water > > > If you have any suggestions I will really appreciate, > > Steven > > > > > > > -- > Javier CEREZO BASTIDA > PhD Student > Physical Chemistry > Universidad de Murcia > Murcia (Spain) > Tel: (+34)868887434 > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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