[gmx-users] Ions and charge groups
Guido Polles
guido.polles at gmail.com
Wed Dec 1 00:42:22 CET 2010
Oh my, you're totally right. I was ignoring that because I had a
coordinate file with hydrogen names from amber, and checking my
coordinate file I realized the atp was after the ions. How
embarrassing. Sorry for wasting your time.
Thank you again
Guido
2010/12/1 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> 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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