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 | ================================================================== -- 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
