Hi Justin Sorry but I don't understand what you mean with "Despite being given the correct settings for CHARMM27, you're still not using them." I use exactly the settings Peter gave me in my last question. What is in this settings wrong and where could I find the right settings?
Greetings Lara ----- Ursprüngliche Message ----- Von: Justin Lemkul <[email protected]> An: Lara Bunte <[email protected]>; Discussion list for GROMACS users <[email protected]> CC: Gesendet: 16:04 Freitag, 21.September 2012 Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error On 9/21/12 9:45 AM, Lara Bunte wrote: > Hello > > My equilibration of water around lumiflavin works (I got no error, no warning > and no note). Sadly the mdrun fails with following error: > > step 886: Water molecule starting at atom 7596 can not be settled. > Check for bad contacts and/or reduce the timestep if appropriate. > > What does GROMACS mean with "check bad contacts" and what do you think I > should fix? > "Bad contacts" refer to atomic clashes that arise either due to insufficient minimization or broken model physics that cause molecules to collide with one another. > > System is lumiflavin in water, CHARMM 27 force field, tip3p water model. > > Here is my mdp file I used before: > > define = -DPOSRES > > integrator = md > dt = 0.002 > emtol = 1000.0 > emstep = 0.01 > nsteps = 5000 > > nstlist = 1 > rlist = 1.2 > rlistlong = 1.4 > rcoulomb = 1.2 > coulombtype = pme > vdw-type = cut-off > rvdw = 1.2 > Despite being given the correct settings for CHARMM27, you're still not using them. It makes it hard to help when you ignore what you've been told. The other option, of course, is that the topology is not sound. How did you derive the parameters for lumiflavin? Have you validated them in any way? Does a simulation of lumiflavin in vacuo succeed? -Justin -- ======================================== Justin A. Lemkul, Ph.D. Research Scientist Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin ======================================== -- 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
