On 2012-09-24 12:34:53PM -0400, Justin Lemkul wrote: > > > On 9/24/12 12:31 PM, Peter C. Lai wrote: > > As I noted before, you can safely ignore the gromacs notices when setting > > them to the correct cutoffs I listed. > > > > Agreed. Please use the cutoffs that have been posted explicitly 3-4 times > now. > > > Your energy minimization still looks a bit high (1000)... > > > > Justin might have some more ideas... > > > > The maximum force is too high. If this condition persists with the proper > cutoffs, then the topology is to blame. You've yet to explain where the > parameters for lumiflavin came from, but if forces are high and the > simulations > collapse, then the parameterization is likely insufficiently accurate.
I was going to suggest running a minimization in double-precision just to check... > > 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 <p...@uab.edu> > >> An: Lara Bunte <lara.bu...@yahoo.de> > >> CC: "gmx-users@gromacs.org" <gmx-users@gromacs.org> > >> 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 <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 | > >> ================================================================== > > > > -- > ======================================== > > 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 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 -- ================================================================== 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
