Re: [gmx-users] mdrun error after 2.6nS

Hello Mark and Tsjerk, Thanks a lot for your suggestions. I have gone through that web site and it doesn't say anything very specific, for example if the system is not minimized properly it should have complained at the beginning, but the problem arises after 2.6nS! I have searched in the archive,

[gmx-users] mdrun error after 2.6nS

   = 250xtc_grps = Proteinenergygrps  = Protein non-proteinnstlist                    = 10 Blaise Mathias Costa, PhDDepartment of Pharmacology and Experimental NeuroscienceUniversity of Nebraska Medical CenterOmaha, NE 68198-5800, USA.Tel: 001 402 559 7132

[gmx-users] g_lie problem

hello all,In my ligand enzyme simulation, I have given energygrps: protein non protein.  The reason is that when I gave energygrps give as : Protein DRG SOL CL, the mdrun stopped at 560ps saying that the system is physically unrealistic! Now I want to analyze the g_lie for the ligand, is there any

[gmx-users] Problem with mdrun!

Hello All,The program was stopped twice with the following error:   Constraint error in algorithm Lincs at step 54646t = 109.292 ps: Water molecule starting at atom 13293 can not be settled.Check for bad contacts and/or reduce the timestep.Wrote pdb files with previous and current coordinatesGrid:

[gmx-users] ligand topology

hello all,How to get the topology for a ligand, for which there is no information available with the gromacs default libraries!! Thanks in advanceBlaise___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users P