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.
-Justin
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
========================================
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