Hi,
So it is not a charge group problem then.
You also don't have pair interactions that act on much longer distances than
atoms separated by 4 bonds?
Berk
Date: Wed, 4 Mar 2009 05:33:15 -0800
From: [email protected]
Subject: RE: [gmx-users] How to overcome Fatal error of bonded interactions
Gromacs 4.0.3
To: [email protected]
Hello,
by charge groups you are referring to charge group number (cgnr) in the
topology file.
Every single atom in my chains belongs to a different charge group. My chains
are polymer ones (identical) with 455 atoms each. A sample of my topology file
is the following:
[ atoms ]
; nr type resnr residu atom cgnr charge
1 CH3 1 a1_pp C1 1 0.000
2 CH3 1 a1_pp C2 2 0.000
3 H 1 a1_pp H3
3 0.000
4 C 1 a1_pp C4 4 0.000
5 H 1 a1_pp H5 5 0.000
6 H 1 a1_pp H6 6 0.000
7 C 1 a1_pp C7 7 0.000
...
I think that that way I do not have big charge groups. My simulations seem
reasonable using this notation.
Thank you,
Nikos
--- Berk Hess <[email protected]> schrieb am Mi,
4.3.2009:
Von: Berk Hess <[email protected]>
Betreff: RE: WG: RE: [gmx-users] How to overcome Fatal error of bonded
interactions Gromacs 4.0.3
An: "Discussion list for GROMACS users" <[email protected]>
Datum: Mittwoch, 4. März 2009, 14:00
Hi,
The question is not if you are using electrostatics or not, but how large your
charge groups are
(a better name for charge groups in Gromacs would be neighbor search groups).
The warning you get is for bonded interactions, but it will usually mean that
your system
is exploding.
Because changing table-extension solved your problem, one guess would be that
you have
too large charge groups, causing non-bonded interactions to be at a too long
distance,
which makes your system explode, which in turn gives the bonded interaction
error.
Berk
Date: Wed, 4 Mar 2009 03:48:33 -0800
From: [email protected]
Subject: WG: RE: [gmx-users] How to overcome Fatal error of bonded
interactions Gromacs 4.0.3
To: [email protected]
--- Claus Valka <[email protected]> schrieb am Mi, 4.3.2009:
Von: Claus Valka <[email protected]>
Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions
Gromacs 4.0.3
An: "Berk Hess" <[email protected]>
Datum: Mittwoch, 4. März 2009, 12:47
Dear Sir Berk,
Thank you for your quick response.. I simulate a system which has 80 chains in
total each having 455 atoms. I do not use any
electrostatics. The box size vary in each direction with the biggest dimension
to be less than 30nm.
The function I'm using is switch. The cut-off I'm using is 0.895nm. I also have
frozen the 64 chains in freezegrps option in the mdp file in all directions.
Judging from what you are telling me, I deduce that I correctly assign the
table-extension parameter big enough. I'm not interested in taking into account
LJ interactions (either pairs or not) that are more than my cut-off distance.
So not even to mention in a distance bigger than: table-ext+cut off.
Also reading again the error it is referring to bonded interactions...
Yours SIncerely,
Nikos
--- Berk Hess
<[email protected]> schrieb am Mi, 4.3.2009:
Von: Berk Hess <[email protected]>
Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions
Gromacs 4.0.3
An: [email protected]
Datum: Mittwoch, 4. März 2009, 12:21
Hi,
table-extension affects the tables for both pair and non-bonded ionteractions.
non-bonded interactions use tables when you use, shift, switch, PME or user
potentials.
You are not by chance simulating large molecules which consist of a single
charge group
or of very large charge groups?
Berk
Date: Wed, 4 Mar 2009 03:12:19 -0800
From: [email protected]
Subject: RE: [gmx-users] How to overcome Fatal error of bonded interactions
Gromacs 4..0.3
To: [email protected]
Hello,
the system I'm referring at is an already equilibrated one. Before, I had
already made steepest
descents.
You are correct that I have non-bonded interactions at distances that are more
than cut-off+table ext distance. I used to put table ext very bin in contrast
to my box. My system box was something less than 5nm before and table-ext was
5nm at the time. Now that I simulate a much bigger system than before (in one
dimension 6 times bigger), I realized that I had to increase also this
parameter.
Since this parameter affects only the pairs interactions I do not see the
reason why my simulations are affected by it, even if it is already big enough
(5nm in a 30nm box). My pairs interactions are (should) not (be) more that 1nm
far away..
I had extensively tested this parameter in gromacs 3, and I saw that it
affects the pairs interactions only. So I decided to increase it very much and
not bother with it.
Is there any difference in newest versions? Does it affect anything more?
Thank you,
Nikos
--- Berk Hess <[email protected]> schrieb am Mi, 4.3.2009:
Von: Berk Hess <[email protected]>
Betreff: RE: [gmx-users] How to overcome Fatal error of bonded interactions
Gromacs 4.0.3
An: "Discussion list for GROMACS users" <[email protected]>
Datum: Mittwoch, 4. März 2009, 9:23
Hi,
Your solution seems to indicate that your system is unstable.
My guess is that your system was not well equilibrated and at some point
some non-bonded interactions were at a distance of more than cut-off+tab_ext.
That would make your system explode. In that case increasing tab_ext to 2 nm
should also suffice.
Berk
Date: Tue, 3 Mar 2009 08:33:52 -0800
From: [email protected]
To: [email protected]
Subject: [gmx-users] How to overcome Fatal error of bonded interactions Gromacs
4.0.3
Hello,
this has to do with my personal experience of using Gromacs version
4.0.3. So this is not an
official response.
The story:
While I was trying to run an NVT simulation in a monoclinic box I encountered
the following problem:
Fatal error:
25 of the 336080 bonded interactions could not be calculated because some atoms
involved moved further apart than the multi-body cut-off distance (0.895 nm) or
the two-body cut-off distance (0.895 nm), see option -rdd, for pairs and
tabulated bonds also see option -ddcheck
and the:
Not all bonded interactions have been properly assigned to the domain
decomposition cells
Trying to put aside the fact that my system had any bug I found in the net the
following:
http://www.gromacs.org/pipermail/gmx-developers/2008-January/002373.html
In order to overcome this error I increased the value of
table-extension = 30
in my mdp file in such a way, as to be bigger from my biggest dimension I had
in my system. The ran proceeded (until now that I'm writing this e-mail)
without any problem.
This value has to do with the cut-off of pairs1-4 LJ interactions and is
calculated in nm.
JFYI
Regards,
Nikos
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