[gmx-users] Water molecule can not be settled - mdrun error

Peter C. Lai pcl at uab.edu
Mon Sep 24 18:31:32 CEST 2012


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 <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            |
> ==================================================================

-- 
==================================================================
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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