[gmx-users] Water molecule can not be settled - mdrun error
lara.bunte at yahoo.de
Mon Sep 24 17:44:18 CEST 2012
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.
----- 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.
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.
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
Peter C. Lai | University of Alabama-Birmingham
Programmer/Analyst | KAUL 752A
Genetics, Div. of Research | 705 South 20th Street
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