[gmx-users] Water molecule can not be settled - mdrun error
Peter C. Lai
pcl at uab.edu
Mon Sep 24 18:38:52 CEST 2012
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 <pcl at uab.edu>
> >> An: Lara Bunte <lara.bunte at yahoo.de>
> >> CC: "gmx-users at gromacs.org" <gmx-users at 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 <pcl at uab.edu>
> >>> An: Lara Bunte <lara.bunte at yahoo.de>
> >>> CC: "gmx-users at gromacs.org" <gmx-users at 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 <pcl at uab.edu>
> >>>> An: Discussion list for GROMACS users <gmx-users at gromacs.org>
> >>>> CC: Lara Bunte <lara.bunte at 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
> >>>> pcl at 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
> >>> pcl at 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
> >> pcl at 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
>
> ========================================
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--
==================================================================
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
pcl at uab.edu | Birmingham AL 35294-4461
(205) 690-0808 |
==================================================================
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