Then yes, your cutoffs are still wrong. However check to see if atom 8376 is clashing with something nearby (protein?). You also never gave any data about the result of the previous energy minimization steps...
On 2012-09-24 04:54:13PM +0100, Lara Bunte wrote: > Hi Peter > > My complete .mdp file is now: > > define = -DPOSRES > > integrator = md > dt = 0.002 > emtol = 1000.0 > emstep = 0.01 > nsteps = 5000 > > nstlist = 1 > rlist = 1.5 > rlistlong = 1.4 > rcoulomb = 1.5 > coulombtype = pme > vdw-type = switch > rvdw_switch = 0.8 > rvdw = 1.5 > > nstxout = 100 > nstvout = 100 > nstenergy = 100 > nstlog = 100 > > tcoupl = V-rescale > tc-grps = ISO SOL > tau_t = 0.1 0.1 > ref_t = 300 300 > > pcoupl = no > > Greetings > Lara > > > > > > > > ----- Ursprüngliche Message ----- > Von: Peter C. Lai <p...@uab.edu> > An: Lara Bunte <lara.bu...@yahoo.de> > CC: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > Gesendet: 17:46 Montag, 24.September 2012 > Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error > > Is this energy minimization or actual integrator = md? > > On 2012-09-24 04:44:18PM +0100, Lara Bunte wrote: > > Hello > > > > Okay, I changed it to > > > > nstlist = 1 > > rlist = 1.5 > > rlistlong = 1.4 > > rcoulomb = 1.5 > > coulombtype = pme > > vdw-type = switch > > rvdw_switch = 0.8 > > rvdw = 1.5 > > > > in my .mdp file and I got now this error: > > > > step 1352: Water molecule starting at atom 8376 can not be settled. > > Check for bad contacts and/or reduce the timestep if appropriate. > > Wrote pdb files with previous and current coordinates > > > > Are the .mdp Options still a problem? > > > > > > I am really thankful for the big amount of help. Thank you. > > Lara > > > > > > > > > > > > > > ----- Ursprüngliche Message ----- > > Von: Peter C. Lai <p...@uab.edu> > > An: Discussion list for GROMACS users <gmx-users@gromacs.org> > > CC: Lara Bunte <lara.bu...@yahoo.de> > > Gesendet: 22:13 Freitag, 21.September 2012 > > Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error > > > > On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote: > > > > > > > > > On 9/21/12 1:31 PM, Lara Bunte wrote: > > > > Hi Justin > > > > > > > > I used this settings except of vdw-type = switch and rvdw_switch = 0.8 > > > > and with this settings grompp gives me two notes and one of this notes > > > > is inconsistent: > > > > > > > > NOTE 1 [file pr.mdp]: > > > > For energy conservation with switch/shift potentials, rlist should > > > >be 0.1 > > > > to 0.3 nm larger than rvdw. > > > > > > > > Because I thought rlist hast to be 1.2 and rvdw hast to be 1.2 for my > > > > CHARMM27 force field. > > > > > > > > > > > > > > Increase rlist as suggested to accommodate the algorithm. Since CHARMM > > > does not > > > use charge groups (well, it uses single-atom charge groups) this isn't > > > such a > > > big deal. For a force field like Gromos96, it matters a lot more. > > > > Actually rlist has to be equal to rvdw for this case (PME will complain if > > it > > doesn't). I haven't had a water settling issue in a correctly setup system > > with rlist = rvdw and a switched rvdw. I do remember a bug in the code that > > forgets rlistlong is specified. > > > > > > > > > > > > > My second note is: > > > > > > > > NOTE 2 [file pr.mdp]: > > > > The sum of the two largest charge group radii (0.079505) is larger > > > >than > > > > rlist (1.200000) - rvdw (1.200000) > > > > > > > > > > > > which I sadly don't understand. > > > > > > > > > > http://www.gromacs.org/Documentation/Errors?highlight=errors#The_sum_of_the_two_largest_charge_group_radii_(X)_is_larger_than.c2.a0rlist_-_rvdw.2frcoulomb > > > > > > -Justin > > > > > > > I also get this note too, but the sum looks fine to me. If the sum > 0.15 > > then > > it typically indicates chargegroups are being used, which they shouldn't > > for > > charmm-based forcefields, but in this case the distance shown is on the > > order > > of a heavy-h bond. I think the note message is still related to rlist vs. > > rlistlong. > > > > anyway, I routinely ignore both these notes and it hasn't given me problems > > so far. I would still go bck to check the specific water that could not > > settle > > and see what the other particles near it are since that is probably the root > > of the problem. Also, we haven't been told what the results of the energy > > minimzation was... > > > > -- > > ================================================================== > > Peter C. Lai | University of Alabama-Birmingham > > Programmer/Analyst | KAUL 752A > > Genetics, Div. of Research | 705 South 20th Street > > p...@uab.edu | Birmingham AL 35294-4461 > > (205) 690-0808 | > > ================================================================== > > -- > ================================================================== > Peter C. Lai | University of Alabama-Birmingham > Programmer/Analyst | KAUL 752A > Genetics, Div. of Research | 705 South 20th Street > p...@uab.edu | Birmingham AL 35294-4461 > (205) 690-0808 | > ================================================================== -- ================================================================== Peter C. Lai | University of Alabama-Birmingham Programmer/Analyst | KAUL 752A Genetics, Div. of Research | 705 South 20th Street p...@uab.edu | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- gmx-users mailing list gmx-users@gromacs.org 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 gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
