[gmx-users] Genion

Sergio Manzetti sergio.manzetti at fjordforsk.no
Thu Jun 22 14:37:02 CEST 2017


Indeed. Thanks! 


Sergio Manzetti 

[ http://www.fjordforsk.no/logo_hr2.jpg ] 

[ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ |   ] 
Midtun 
6894 Vangsnes 
Norge 
Org.nr. 911 659 654 
Tlf: +47 57695621 
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From: "Mark Abraham" <mark.j.abraham at gmail.com> 
To: "gmx-users" <gmx-users at gromacs.org> 
Sent: Thursday, June 22, 2017 2:29:54 PM 
Subject: Re: [gmx-users] Genion 

Hi, 

The error message has a helpful URL that'll take you to the same advice 
that we give several times a week on here :-) 

Mark 

On Thu, 22 Jun 2017 14:27 Sergio Manzetti <sergio.manzetti at fjordforsk.no> 
wrote: 

> Thanks, Worked out. Now I got a note saying: 
> 
> NOTE 1 [file em.mdp]: 
> The group cutoff scheme is deprecated since GROMACS 5.0 and will be 
> removed in a future release when all interaction forms are supported for 
> the verlet scheme. The verlet scheme already scales better, and it is 
> compatible with GPUs and other accelerators. 
> 
> 
> 
> Fatal error: 
> 1 particles communicated to PME rank 3 are more than 2/3 times the cut-off 
> out of the domain decomposition cell of their charge group in dimension x. 
> This usually means that your system is not well equilibrated. 
> For more information and tips for troubleshooting, please check the GROMACS 
> website at http://www.gromacs.org/Documentation/Errors 
> 
> 
> 
> How can I fix the system, when the energy minimization step cannot? 
> 
> 
> Sergio 
> 
> 
> Sergio Manzetti 
> 
> [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> 
> [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ http://www.fjordforsk.no/ 
> | ] 
> Midtun 
> 6894 Vangsnes 
> Norge 
> Org.nr. 911 659 654 
> Tlf: +47 57695621 
> [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ 
> http://www.phap.no/ | FAP ] 
> 
> 
> 
> From: "Justin Lemkul" <jalemkul at vt.edu> 
> To: "gmx-users" <gmx-users at gromacs.org> 
> Sent: Thursday, June 22, 2017 2:21:17 PM 
> Subject: Re: [gmx-users] Genion 
> 
> On 6/22/17 8:14 AM, Sergio Manzetti wrote: 
> > OK, now I treied writing Na Cl and not NA and CL and get: 
> > 
> 
> This is what you did before, so naturally you get the same thing. 
> 
> > Na) 
> > Warning: atom name 11966 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11967 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11968 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11969 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > Warning: atom name 11970 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> > 
> 
> As I said, using mixed case is incorrect. The [moleculetype] entries in 
> ions.itp expect all caps. Use all caps. 
> 
> -Justin 
> 
> > 
> > 
> > 
> > 
> > Sergio Manzetti 
> > 
> > [ http://www.fjordforsk.no/logo_hr2.jpg ] 
> > 
> > [ http://www.fjordforsk.no/ | Fjordforsk AS ] [ 
> http://www.fjordforsk.no/ | ] 
> > Midtun 
> > 6894 Vangsnes 
> > Norge 
> > Org.nr. 911 659 654 
> > Tlf: +47 57695621 
> > [ http://www.oekolab.com/ | Økolab ] | [ http://www.nanofact.no/ | 
> Nanofactory ] | [ http://www.aq-lab.no/ | AQ-Lab ] | [ http://www.phap.no/ 
> | FAP ] 
> > 
> > 
> > 
> > From: "Justin Lemkul" <jalemkul at vt.edu> 
> > To: "gmx-users" <gmx-users at gromacs.org> 
> > Sent: Thursday, June 22, 2017 2:09:02 PM 
> > Subject: Re: [gmx-users] Genion 
> > 
> > On 6/22/17 7:30 AM, Sergio Manzetti wrote: 
> >> Hi, the procedure as defined by Juistin worked out well. However, a new 
> problem has occurred. At mdrun for the minimization, I get: 
> >> 
> >> ------------------------------------------------------- 
> >> Program gmx mdrun, VERSION 5.1.2 
> >> Source code file: 
> /build/gromacs-z6bPBg/gromacs-5.1.2/src/gromacs/ewald/pme-redistribute.cpp, 
> line: 276 
> >> 
> >> Fatal error: 
> >> 1 particles communicated to PME rank 3 are more than 2/3 times the 
> cut-off out of the domain decomposition cell of their charge group in 
> dimension x. 
> >> This usually means that your system is not well equilibrated. 
> >> For more information and tips for troubleshooting, please check the 
> GROMACS 
> >> website at http://www.gromacs.org/Documentation/Errors 
> >> 
> >> 
> >> This may be caused by the solvent replacement of genion by Na Cl: 
> >> 
> >> 
> >> 
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> >> Reading file dna_solv.tpr, VERSION 5.1.2 (single precision) 
> >> Will try to add 130 Na ions and 90 Cl ions. 
> >> Select a continuous group of solvent molecules 
> >> Group 0 ( System) has 98254 elements 
> >> Group 1 ( DNA) has 1333 elements 
> >> Group 2 ( Water) has 96921 elements 
> >> Group 3 ( SOL) has 96921 elements 
> >> Group 4 ( non-Water) has 1333 elements 
> >> Select a group: 3 
> >> Selected 3: 'SOL' 
> >> Number of (3-atomic) solvent molecules: 32307 
> >> Replacing solvent molecule 3244 (atom 11065) with Na 
> >> Replacing solvent molecule 8993 (atom 28312) with Na 
> >> Replacing solvent molecule 7088 (atom 22597) with Na 
> >> Replacing solvent molecule 29442 (atom 89659) with Na 
> >> Replacing solvent molecule 30079 (atom 91570) with Na 
> >> Replacing solvent molecule 5128 (atom 16717) with Na 
> >> Replacing solvent molecule 10705 (atom 33448) with Na 
> >> Replacing solvent molecule 1418 (atom 5587) with Na 
> >> Replacing solvent molecule 6608 (atom 21157) with Na 
> >> Replacing solvent molecule 28124 (atom 85705) with Na 
> >> Replacing solvent molecule 5440 (atom 17653) with Na 
> >> Replacing solvent molecule 31518 (atom 95887) with Na 
> >> Replacing solvent molecule 16384 (atom 50485) with Na 
> >> Replacing solvent molecule 17675 (atom 54358) with Na 
> >> Replacing solvent molecule 23446 (atom 71671) with Na 
> >> Replacing solvent molecule 15659 (atom 48310) with Na 
> >> Replacing solvent molecule 18442 (atom 56659) with Na 
> >> Replacing solvent molecule 23777 (atom 72664) with Na 
> >> Replacing solvent molecule 5965 (atom 19228) with Na 
> >> Replacing solvent molecule 15375 (atom 47458) with Na 
> >> Replacing solvent molecule 30985 (atom 94288) with Na 
> >> Replacing solvent molecule 19076 (atom 58561) with Na 
> >> Replacing solvent molecule 18065 (atom 55528) with Na 
> >> Replacing solvent molecule 22711 (atom 69466) with Na 
> >> Replacing solvent molecule 27097 (atom 82624) with Na 
> >> Replacing solvent molecule 21561 (atom 66016) with Na 
> >> Replacing solvent molecule 18592 (atom 57109) with Na 
> >> Replacing solvent molecule 22174 (atom 67855) with Na 
> >> Replacing solvent molecule 17888 (atom 54997) with Na 
> >> Replacing solvent molecule 13005 (atom 40348) with Na 
> >> Replacing solvent molecule 3481 (atom 11776) with Na 
> >> Replacing solvent molecule 22603 (atom 69142) with Na 
> >> Replacing solvent molecule 9899 (atom 31030) with Na 
> >> Replacing solvent molecule 3438 (atom 11647) with Na 
> >> Replacing solvent molecule 12180 (atom 37873) with Na 
> >> Replacing solvent molecule 32219 (atom 97990) with Na 
> >> Replacing solvent molecule 23159 (atom 70810) with Na 
> >> Replacing solvent molecule 27929 (atom 85120) with Na.... 
> >> 
> >> 
> >> which then reflects on grompp as: 
> >> 
> >> 
> >> 
> >> Setting the LD random seed to 3274024379 
> >> Generated 2211 of the 2211 non-bonded parameter combinations 
> >> Generating 1-4 interactions: fudge = 0.5 
> >> Generated 2211 of the 2211 1-4 parameter combinations 
> >> Excluding 3 bonded neighbours molecule type 'DNA_chain_E' 
> >> Excluding 3 bonded neighbours molecule type 'DNA_chain_F' 
> >> Excluding 2 bonded neighbours molecule type 'SOL' 
> >> Excluding 1 bonded neighbours molecule type 'NA' 
> >> Excluding 1 bonded neighbours molecule type 'CL' 
> >> Warning: atom name 97595 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97596 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97597 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97598 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97599 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97600 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97601 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97602 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97603 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97604 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97605 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97606 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97607 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97608 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97609 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97610 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97611 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97612 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97613 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> Warning: atom name 97614 in topol.top and dna_solv_NaCl.gro does not 
> match (NA - Na) 
> >> (more than 20 non-matching atom names) 
> >> 
> >> WARNING 1 [file topol.top, line 50]: 
> >> 220 non-matching atom names 
> >> atom names from topol.top will be used 
> >> atom names from dna_solv_NaCl.gro will be ignored 
> >> 
> >> 
> >> 
> >> 
> >> 
> >> Giving the mdrun problem.. 
> >> 
> >> 
> >> Not sure how to get by this! 
> >> 
> > 
> > The mismatching names are not causing the failure. You're getting what 
> you 
> > asked for as you requested "Na" and "Cl" ions be added. This does not 
> match the 
> > convention in ions.itp, which uses "NA" and "CL" for ions (this is a 
> standard 
> > GROMACS thing - elemental symbols in all caps should always be used for 
> -pname 
> > and -nname). But sodium is still sodium and chloride is still chloride, 
> so your 
> > topology is not actually out of step with the coordinates. 
> > 
> > Your initial configuration is simply so you did not adequately minimize 
> or 
> > equilibrate prior to running dynamics, as the mdrun error suggests. 
> > 
> > -Justin 
> > 
> 
> -- 
> ================================================== 
> 
> Justin A. Lemkul, Ph.D. 
> Ruth L. Kirschstein NRSA Postdoctoral Fellow 
> 
> Department of Pharmaceutical Sciences 
> School of Pharmacy 
> Health Sciences Facility II, Room 629 
> University of Maryland, Baltimore 
> 20 Penn St. 
> Baltimore, MD 21201 
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441 
> http://mackerell.umaryland.edu/~jalemkul 
> 
> ================================================== 
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