On 10/18/12 8:51 AM, [email protected] wrote:
Hi Justin,
Well I already tried the protein without the membrane and I got the same
result. And I also make sure that I had no error messages during the
preparation runs.
If the protein crashes in the absence of anything else, then likely you have
problems with its starting geometry. Applying restraints during minimization is
probably causing the clashes to be insufficiently resolved.
I am using the amber03 force field.
My dummy atoms have a radius of 1.00 and a charge of 0.00. And yes they
are non bonded atoms.
Radius of 1.0 nm? If the crash occurs without these atoms, then it's likely
irrelevant, but with particles 10 times the size of normal atoms, you may be
asking for trouble.
-Justin
On 10/18/12 7:05 AM, [email protected] wrote:
Hi Justin,
I already read the page you send me.
And I am sure about the first points. But I am not completely sure about
Sure about the first five points? The five suggestions on the page I
linked are
all diagnostic steps. What did they turn up?
the mdp file for the nvt run.
It looks like this:
define = -DPOSRES
integrator = md
dt = 0.002
nsteps = 10000
nstxout = 0
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 0
nstenergy = 5
energygrps = Protein Non-Protein
nstcalcenergy = 5
nstlist = 10
ns-type = Grid
pbc = xyz
rlist = 0.9
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
gen_vel = yes
gen_temp = 200.0
gen_seed = 9999
constraints = all-bonds
tcoupl = V-rescale
tc-grps = Protein Non-Protein
tau_t = 0.1 0.1
ref_t = 298 298
pcoupl = no
What force field are you using? What about my questions related to your
so-called dummy atoms? What are they and what are their parameters? Your
minimization seemed fine, so there's clearly something wrong with the
physical
model that leads to a crash during MD. At present, there's not enough
information to say exactly what.
-Justin
Thank you for your help,
Eva
On 10/18/12 6:15 AM, [email protected]
wrote:
Hi Erik,
my .mdp file looks like this:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 30000
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
rlist = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
pbc = xyz
And yes, I use constraints. I have a membrane represented by dummy
atoms
around my protein. They are fixed and I also fixed the backbone. Or is
that a problem.
The EM seems to have worked fine, so we need the .mdp file for NVT, not
EM.
Your membrane representation could be an issue, but I'm not clear on
the
terminology here. A "dummy atom" (or virtual site) is a particle with
nonbonded
parameters but no mass. Is that what you're dealing with? If this
membrane
environment is fixed and the backbone is too, you may get clashes in
the
system,
but it doesn't sound like there's a whole lot that's moving in the
first
place.
General troubleshooting advice (that I seem to post almost daily):
http://www.gromacs.org/Documentation/Terminology/Blowing_Up#Diagnosing_an_Unstable_System
Your simulation is failing fairly early, so finding the source of the
crash
should not be terribly difficult.
-Justin
It could be due to your mdp-settings. What's your time step? Do you
use
constraints and virtual interaction sites?
Erik
18 okt 2012 kl. 12.04 skrev
[email protected]:
Hi Felix,
thank you for your answer.
So you think that a force of 3.2341940e+02 is okey? To work on?
I also tried to work on with a NVT run but then I got many many
LINCS
warnings:
Step 1114, time 2.228 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000169, max 0.001796 (between atoms 3480 and 3482)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
3480 3482 30.3 0.1090 0.1092 0.1090
Step 1121, time 2.242 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.000108, max 0.000561 (between atoms 2000 and 2001)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
2002 2005 30.4 0.1090 0.1090 0.1090
And in the end there is the error:
Fatal error:
11 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposit
ion cell of their charge group in dimension x.
I looked it up on the GROMACS site and it was written there that
such
a
error is caused by a not well equilibrated system.
So I thought that the high force might be the reason.
What do you think?
Thanks again!!
Hi Eva,
The change in energy in every step became smaller than the machine
precision can represent (as is stated in the output). In other
words:
your
system is minimized to a very high degree.
A value of 10 for the Fmax is very low for a system like yours,
even
with
a pure protein in water system you probably wouldn't hit this
value.
Furthermore, 30.000 steps for a minimization seems pretty high to
me.
Cheers,
Felix
-----Ursprüngliche Nachricht-----
Von: [email protected]
[mailto:[email protected]]
Im Auftrag von [email protected]
Gesendet: Donnerstag, 18. Oktober 2012 10:56
An: [email protected]
Betreff: [gmx-users] question about the minimization
Hi everybody,
I have a question about the minimization of my protein. For this
minimization I fixed the backbone and the membrane atoms which
around
my
protein.
I minimized it 30000 steps long but after step 20385 it stops with
the
output:
Steepest Descents converged to machine precision in 20385 steps,
but
did
not reach the requested Fmax < 10.
Potential Energy = -8.8805600e+05
Maximum force = 3.2341940e+02 on atom 3050
Norm of force = 2.0930219e+00
I do not see why it can not reach a lower force.
I already looked at the structure with Pymol and there I saw that
the
atom
3050 is in a loop and do not interact with any other residue.
My .mdp file looks like this:
define = -DPOSRES
integrator = steep
emtol = 10
nsteps = 30000
nstenergy = 1
energygrps = System
coulombtype = PME
rcoulomb = 0.9
rvdw = 0.9
rlist = 0.9
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
pbc = xyz
Do you see a reason why it can not reach a force lower than 10?
Thank you,
Eva
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-----------------------------------------------
Erik Marklund, PhD
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: +46 18 471 6688 fax: +46 18 511 755
[email protected]
http://www2.icm.uu.se/molbio/elflab/index.html
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--
========================================
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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========================================
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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========================================
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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