[gmx-users] Ions and charge groups
Justin A. Lemkul
jalemkul at vt.edu
Wed Dec 1 00:14:51 CET 2010
Guido Polles wrote:
> 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.
>
Did you get any warnings from grompp that the names in the coordinate file and
topology did not match? My guess is yes. The [molecules] directive must match
the order of the coordinate file, otherwise the wrong parameters are applied to
the wrong species. If this is the case, the bonds involving CL were a result of
SOL (water) bonded parameters being applied to CL atoms.
-Justin
> 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" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Ions and charge groups
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4CF54C0D.9070001 at vt.edu>
> 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
>
> ========================================
--
========================================
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
========================================
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