Hi, thanks for the very fast reply.
I used pdb2gmx just to build the protein. Then i wrote my own topology
including the itp file for the protein and for the atp molecule. I
added the ions then.
From a pdb file I solvated proteon(6 proteins)+atp+ions and added the
water to the top file, that came to look something like
[ system ]
; Name
system in water
[ molecules ]
; Compound #mols
protein 6
atp 1
CL 48
K 16
SOL 53231
This way, I get that weird behavior about bonds for CL atoms.
Doing a couple of further tests I actually solved the problem
inverting water and ions both in coordinates and topology, i.e.
[ molecules ]
; Compound #mols
protein 6
atp 1
SOL 53231
CL 48
K 16
Everything now is fine, I successfully minimized and running a short
simulation doesn't complain about anything.
I think is a pretty strange behavior and I don't understand why I'm
forced to put ions after water.
Looks like a little bug to me, but I'm not expert enough to be sure.
Anyway, thank you a lot for your help.
Guido
Guido Polles wrote:
Hi everybody,
Sorry about this, but I'm pretty new to gromacs and I couldn't find
any clue about my problem in the archives or in the manual.
I'm using gromacs 4.5.1, and my system is a rather big system (about
12x12x12) that includes a proteon, an atp molecule, water and some
ions.
I am using ffamber99sb force field. Now, I post the log for my mdrun.
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685
multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686
Minimum cell size due to bonded interactions: 16.294 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2 cells with a minimum initial size of 20.368 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0
-------------------------------------------------------
Program mdrun, VERSION 4.5.1
Source code file: domdec.c, line: 6428
Fatal error:
There is no domain decomposition for 2 nodes that is compatible with
the given box and a minimum cell size of 20.368 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Of course the main point here is this
Initial maximum inter charge-group distances:
two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685
multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686
but they're CL ions! Why should they have any bonded interaction or
angle interaction??
They shouldn't. Check your [bonds] and [angles] directives for these atom
numbers. Apparently mdrun is finding bonds to these ions in your topology.
Were these ions added with genion? Present in the initial structure processed
by pdb2gmx? Manually added in some location?
Actually, I made some tests, and:
1- if I solvate the protein+atp+ions (I want the ions to be in
specific positions) system I get that 14nm bond error when I run
mdrun, but grompp let it go.
OK, so you want ions in specific positions. Did you put them there? If so, was
it before or after you generated the topology (presumably with pdb2gmx)?
2- in this situation, if I move in the gro file the coords for the
ions after the water, same happens but now grompp throws a warning
about charge group distance.
That's probably related to the contents of your .mdp file, which you haven't
posted. It may or may not be related to the problem at hand.
3- if I solvate then use genion to include the ions at least the
simulation starts. Then I get this error "A charge group moved too far
between two domain decomposition steps", but that is probably related
to my system
That error message indicates your system has become unstable, likely due to
insufficient energy minimization or equilibration, or incorrect .mdp settings.
http://www.gromacs.org/Documentation/Terminology/Blowing_Up
-Justin
I really don't get what's going on here.
Thank you in advance for any feedback.
Guido
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
------------------------------
Message: 3
Date: Tue, 30 Nov 2010 14:10:05 -0500
From: "Justin A. Lemkul" <[email protected]>
Subject: Re: [gmx-users] Ions and charge groups
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[email protected]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Justin A. Lemkul wrote:
Guido Polles wrote:
Hi everybody,
Sorry about this, but I'm pretty new to gromacs and I couldn't find
any clue about my problem in the archives or in the manual.
I'm using gromacs 4.5.1, and my system is a rather big system (about
12x12x12) that includes a proteon, an atp molecule, water and some
ions.
I am using ffamber99sb force field. Now, I post the log for my mdrun.
Initializing Domain Decomposition on 2 nodes
Dynamic load balancing: auto
Will sort the charge groups at every domain (re)decomposition
Initial maximum inter charge-group distances:
two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685
multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686
Minimum cell size due to bonded interactions: 16.294 nm
Using 0 separate PME nodes
Scaling the initial minimum size with 1/0.8 (option -dds) = 1.25
Optimizing the DD grid for 2 cells with a minimum initial size of
20.368 nm
The maximum allowed number of cells is: X 0 Y 0 Z 0
-------------------------------------------------------
Program mdrun, VERSION 4.5.1
Source code file: domdec.c, line: 6428
Fatal error:
There is no domain decomposition for 2 nodes that is compatible with
the given box and a minimum cell size of 20.368 nm
Change the number of nodes or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition
For more information and tips for troubleshooting, please check the
GROMACS
website at http://www.gromacs.org/Documentation/Errors
Of course the main point here is this
Initial maximum inter charge-group distances:
two-body bonded interactions: 14.813 nm, LJ-14, atoms 25682 25685
multi-body bonded interactions: 14.813 nm, Angle, atoms 25685 25686
but they're CL ions! Why should they have any bonded interaction or
angle interaction??
They shouldn't. Check your [bonds] and [angles] directives for these
atom numbers. Apparently mdrun is finding bonds to these ions in your
topology. Were these ions added with genion? Present in the initial
structure processed by pdb2gmx? Manually added in some location?
Actually, I made some tests, and:
1- if I solvate the protein+atp+ions (I want the ions to be in
specific positions) system I get that 14nm bond error when I run
mdrun, but grompp let it go.
OK, so you want ions in specific positions. Did you put them there? If
so, was it before or after you generated the topology (presumably with
pdb2gmx)?
Also relevant here, but I forgot to ask: are you using distance restraints to
keep these ions in place? If so, that's your problem. If the restraints can't
be placed in the same DD cell, you have to use particle decomposition (mdrun
-pd), which is somewhat slower.
-Justin
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
