As I noted before, you can safely ignore the gromacs notices when setting them to the correct cutoffs I listed.
Your energy minimization still looks a bit high (1000)... Justin might have some more ideas... On 2012-09-24 05:07:59PM +0100, Lara Bunte wrote: > Hi > > The result of the energy minimization before is: > > Steepest Descents: > Tolerance (Fmax) = 1.00000e+03 > Number of steps = 5000 > > Stepsize too small, or no change in energy. > Converged to machine precision, > but not to the requested precision Fmax < 1000 > > Double precision normally gives you higher accuracy. > You might need to increase your constraint accuracy, or turn > off constraints alltogether (set constraints = none in mdp file) > > writing lowest energy coordinates. > > Steepest Descents converged to machine precision in 226 steps, > but did not reach the requested Fmax < 1000. > Potential Energy = -1.3277053e+05 > Maximum force = 1.7070897e+03 on atom 8 > Norm of force = 3.8431282e+01 > > My System is lumiflavin in water, tip3p water model and charmm27 force field. > My actual goal is to equilibrate the water around the lumiflavin with that > .mdp file I wrote. What is now wrong with the cut-offs? If I use the settings > for charmm27 cut-offs you wrote I got all that problems I wrote. Would you > please change here how it should look like: > > > 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 > > I am totaly frustrated and shortly for giving it up :-(:-( :-( > > Best greetings > Lara > > > > > > > > > > > ----- Ursprüngliche Message ----- > Von: Peter C. Lai <[email protected]> > An: Lara Bunte <[email protected]> > CC: "[email protected]" <[email protected]> > Gesendet: 17:57 Montag, 24.September 2012 > Betreff: Re: [gmx-users] Water molecule can not be settled - mdrun error > > 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 <[email protected]> > > An: Lara Bunte <[email protected]> > > CC: "[email protected]" <[email protected]> > > 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 <[email protected]> > > > An: Discussion list for GROMACS users <[email protected]> > > > CC: Lara Bunte <[email protected]> > > > 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 > > > [email protected] | 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 > > [email protected] | 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 > [email protected] | 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 [email protected] | Birmingham AL 35294-4461 (205) 690-0808 | ================================================================== -- 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
