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

[Lara Bunte]

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            |
==================================================================