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 <jalem...@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" <jalem...@vt.edu> >> Subject: Re: [gmx-users] Ions and charge groups >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Message-ID: <4cf54c0d.9070...@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 > > ======================================== > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. 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