Re: [gmx-users] segmentation fault on gromacs 4.5.5 after mdrun

On 11/11/13 11:24 AM, Carlos Javier Almeciga Diaz wrote: Hello evryone, I doing a simulation of a ligand-protein interaction with gromacs 4.5.5. Everything looks fine after I equilibrate the protein-ligand complex. I'm running these commands: grompp -f nvt.mdp -c em.gro -p topol.top -n ind

Re: [gmx-users] segmentation fault on g_protonate

On 8/9/13 2:35 PM, Pedro Lacerda wrote: Hi, My heteromolecule structure is missing hydrogens. I did an aminoacids.hdb entry which I suppose being right. When running `g_protonate -s conf.pdb -o prot.pdb` to add the hydrogens happens an segmentation fault. The traceback for 4.6.4-dev-20130808-a

Re: [gmx-users] Segmentation fault (core dumped)

On 6/6/13 4:45 AM, Ishwor Poudyal wrote: Dear all I want to study the diffusion coeffcient of CO in water. I have done the energy minimization step and got the problem segmentation fault during Equilibration. I am confused whether my input file has got some error or the err

Re: [gmx-users] segmentation fault

On 11/29/12 10:44 AM, Shine A wrote: Sir, I have one more doubt. During NVT equilibration mdrun giving segmentation fault and not generating any gro files and generating two pdb files. The message is like this Wrote pdb files with previous and current coordinates Warning: 1-4 int

Re: [gmx-users] Segmentation fault while calculating water mediated H-bond with g_hbond

There were a few bugfixes done to g_hbond since 4.5.3. Try a more recent version. Erik 23 okt 2012 kl. 17.41 skrev bipin singh: > Hello all, > > I was trying to calculate solvent mediated H-bond between a amino acid > residue (Tyr) and solvent molecule present within cutoff of 0.5nm (after >

RE: [gmx-users] Segmentation fault (core dumped error)

Thanks very much for much for your help. The Carbon naotube issue is solved. I still have to figure out the polymers. Thanks for the info Regards Elie > Date: Fri, 14 Sep 2012 10:31:28 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] Segmentation

Re: [gmx-users] Segmentation fault (core dumped error)

On 9/14/12 12:19 AM, Elie M wrote: Dear all, I am trying to study the MD of a Carbon Nanotube interacting with some polymers. and I have some problems in forming the topology files. I have actually two questions and I hope you can help me in that. (1) In an attempt to form the topology files

Re: [gmx-users] segmentation fault with mdrun

On 8/21/12 6:00 AM, Deepak Ojha wrote: Dear All I am trying to perform the azide ion in water simulation with Gromacs. I generated to topology file with PRODG server for azide ion and ran the calculations.I got one error at grompp level which was " 327 non-matching atom names atom nam

Re: [gmx-users] segmentation fault during equilibration

On 5/1/12 2:50 PM, niaz poorgholami wrote: Dear Justin the results of EM was: Steepest Descents converged to Fmax< 1000 in 77 steps Potential Energy = -3.6802272e+05 Maximum force = 8.9652832e+02 on atom 1556 Norm of force = 1.1512711e+02 thank you for your concern All of that s

Re: [gmx-users] segmentation fault during equilibration

On 5/1/12 1:13 PM, niaz poorgholami wrote: thank you Sir for your reply.below I provide you .mdp file: title = UNK-ligand complex NVT equilibration define = -DPOSRES -DPOSRES_LIG ; position restrain the UNK and LIG ; Run parameters integrator = md; leap-frog integrator n

Re: [gmx-users] segmentation fault during equilibration

On 5/1/12 7:19 AM, niaz poorgholami wrote: Dear gmx users, I am simulating a system including carbon nanotube(a finite one)+water+surfactant and so far I have done these things: 1.I generated the topology of CNT ( opls force field) by this command: g_x2top -f cnt.pdf -o cnt.top -nopairs -nexcl

Re: [gmx-users] segmentation fault

priya thiyagarajan wrote: hello sir, thanks for your kind reply.. in another folder i resubmitted my mdrun from starting time.. i reduced my time step.. i kept my time step = 0.001 this is my md.mdp file title= Gromacs43a1 lipopeptide MD ; Run parameters integrator= md

Re: [gmx-users] Segmentation Fault using g_cluster

mx-users@gromacs.org>> Date: Wed, 28 Mar 2012 13:29:40 +1100 To: Discussion list for GROMACS users <mailto:gmx-users@gromacs.org>> Subject: Re: [gmx-users] Segmentation Fault using g_cluster On 28/03/2012 1:00 PM, Davide Mercadante wrote: Dear Gromacs Users, I am trying to run g_clu

Re: [gmx-users] Segmentation Fault using g_cluster

Wed, 28 Mar 2012 13:29:40 +1100 To: Discussion list for GROMACS users Subject: Re: [gmx-users] Segmentation Fault using g_cluster On 28/03/2012 1:00 PM, Davide Mercadante wrote: > > Dear Gromacs Users, > > > > > I am trying to run g_cluster to find an avera

Re: [gmx-users] Segmentation Fault using g_cluster

On 28/03/2012 1:00 PM, Davide Mercadante wrote: Dear Gromacs Users, I am trying to run g_cluster to find an average structure for my system and after giving the following command line: g_cluster_d -f allnj10_XM10.xtc -s EB_XM.gro -cl pdb_ligplot_XM.pdb -n --g g_cluster started without proble

Re: [gmx-users] Segmentation fault

saly jackson wrote: Hi all Would you please let me know how can I remove the following error when I want to run 'mdrun -v -deffnm H'? Back Off! I just backed up H.log to ./#H.log.1# Getting Loaded... Reading file H.tpr, VERSION 4.5.4 (single precision) Starting 24 threads Segmentation faul

Re: [gmx-users] Segmentation fault

On 9/03/2012 6:24 PM, rama david wrote: Hi , Thank you for help. I solve my problem for LINCS error But now I have another problem after mdrun command gromacs output Making 1D domain decomposition 4 x 1 x 1 starting mdrun 'Martini system from nap.pdb' 5000 steps,100.0 ps. step 0Segmen

Re: [gmx-users] segmentation fault err

On 6/03/2012 2:58 AM, shilpa yadahalli wrote: Dear gmx-users, I'm facing "segmentation fault error" while *mdrun*. When i checked my md.log file, after 440'th step the kinetic energy energy increases by tenfold and hence the temperature (temp - 6.80141e+01K to 2.21829e+02K). all other values,

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 10:26 PM, Mark Abraham wrote: > On 2/03/2012 9:22 AM, Steven Neumann wrote: > > > > On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul wrote: > >> >> >> Steven Neumann wrote: >> >>> >>> >>> On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul >> jalem...@vt.edu>> wrote: >>> >>>

Re: [gmx-users] Segmentation fault - Implicit solvent

On 2/03/2012 9:22 AM, Steven Neumann wrote: On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul mailto:jalem...@vt.edu>

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 10:07 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul > jalem...@vt.edu>> wrote: >> >> >> >>Steven Neumann wrote: >> >> >> >>On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann >>mailto:s.neu

Re: [gmx-users] Segmentation fault - Implicit solvent

Steven Neumann wrote: On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul > wrote: Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann mailto:s.neuman...@gmail.com>

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 5:43 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> >> >> On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann > s.neuman...@gmail.com>**> wrote: >> >> >> >>On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann >>mailto:s.neuman...@gmail.com>**> wrote: >> >> >> >>

Re: [gmx-users] Segmentation fault - Implicit solvent

Steven Neumann wrote: On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann > wrote: On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann mailto:s.neuman...@gmail.com>> wrote: On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul mailto:jalem...@vt.e

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 3:58 PM, Steven Neumann wrote: > > > On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann wrote: > >> >> >> On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul wrote: >> >>> >>> >>> Steven Neumann wrote: >>> Dear Gmx Users, I am trying to run nvt simulation (equilibratio

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 3:32 PM, Steven Neumann wrote: > > > On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul wrote: > >> >> >> Steven Neumann wrote: >> >>> Dear Gmx Users, >>> I am trying to run nvt simulation (equilibration) of the protein in >>> implicit solvent. My mdp: >>> >>> integrator =

Re: [gmx-users] Segmentation fault - Implicit solvent

On Thu, Mar 1, 2012 at 2:55 PM, Justin A. Lemkul wrote: > > > Steven Neumann wrote: > >> Dear Gmx Users, >> I am trying to run nvt simulation (equilibration) of the protein in >> implicit solvent. My mdp: >> >> integrator = md ; leap-frog integrator >> >> nsteps = 100 ; 0.0005 * 100 = 0.

Re: [gmx-users] Segmentation fault - Implicit solvent

Steven Neumann wrote: Dear Gmx Users, I am trying to run nvt simulation (equilibration) of the protein in implicit solvent. My mdp: integrator = md ; leap-frog integrator nsteps = 100 ; 0.0005 * 100 = 0.5 ns dt = 0.0005 ; 0.5 fs ; Output control nstxout = 1 nstxtcout = 1

Re: [gmx-users] Segmentation fault

On 2/01/2012 12:35 AM, Saba Ferdous wrote: Dear Gromacs Experts, I am having problem in execution of a command in Gromacs, thats when i use dssp for secondary structure analysis. it gives error: Reading file md_0_10.tpr, VERSION 4.5.5 (single precision) Reading file md_0_10.tpr, VERSION 4.5.

Re: [gmx-users] Segmentation fault error from mdrun

On 8/12/2011 7:36 AM, rainy908 wrote: Hi, I encounter the following error when trying to execute mdrun: # Running Gromacs: read TPR and write output to /gpfs disk $MPIRUN $MDRUN -v -nice 0 -np $NSLOTS \ -s n12_random_50_protein_all.tpr \ -o n12_random_50_protein_all.trr \ -c n12_random

Re: [gmx-users] segmentation fault from power6 kernel

bre 2011 14:40:39 Oggetto: Re: [gmx-users] segmentation fault from power6 kernel On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Pleas

Re: [gmx-users] segmentation fault from power6 kernel

On 3/11/2011 7:59 PM, Fabio Affinito wrote: Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Sounds like a bug. Please file a report here http://redmine.gromacs.org including you

Re: [gmx-users] segmentation fault from power6 kernel

Thank you, Mark. Using GMX_NOOPTIMIZEDKERNELS=1 everything runs fine on power6. I also tried to run on a linux cluster and it went ok. Fabio The most likely issue is some normal "blowing up" scenario leading to a table-lookup-overrun segfault in the 3xx series kernels. I don't know why the us

Re: [gmx-users] segmentation fault from power6 kernel

On 3/11/2011 6:42 AM, Fabio AFFINITO wrote: Dear all, I've trying to run a simulation on a IBM Power6 cluster. At the beginning of the simulation I've got a segmentation fault. I investigated with TotalView and I've found that this segmentation violation originates in the pwr6kernel310.F Up to

Re: [gmx-users] Segmentation fault after mdrun for MD simulation

On 18/08/2011 2:41 PM, rainy908 wrote: Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md

Re: [gmx-users] Segmentation fault after mdrun for MD simulation

Hi Justin, THanks for the input. So I traced back to my energy minimization steps, and am getting the error message after I execute the following line: $mdrun -s 1JFF_em.tpr -o 1JFF_em.trr -c 1JFF_b4pr.gro -e em.edr output: Back Off! I just backed up md.log to ./#md.log.2# Reading file 1JFF_em

Re: [gmx-users] Segmentation fault after mdrun for MD simulation

rainy908 wrote: Dear gmx-users: Thanks Justin for your help. But now I am experiencing a Segmentation fault error when executing mdrun. I've perused the archives but found none of the threads on segmentation faults similar to my case here. I believe the segmentation fault is caused by th

Re: [gmx-users] Segmentation fault

Sayan Bagchi wrote: Hello All, I was trying to run a MD simulation of a 17 amino acid peptide. At the position restraint step, the program crashed after running ~536 ps. It gave the error message: "t=536.242 ps: Water molecule starting at atom 6101 cannot be settled. Check for bad contacts

Re: [gmx-users] segmentation fault.

sreelakshmi ramesh wrote: dear gmx-users, During equilibriation i get the following error.Any suggestions please. *grompp* WARNING 1 [file npt.mdp]: The sum of the two largest charge group radii (2.369582) is larger than rlist (1.00) This message suggest

Re: [gmx-users] segmentation fault: g_velacc

Thanks very much, Dr. Kutzner! On Tue, Feb 1, 2011 at 9:14 PM, Carsten Kutzner wrote: > Hi Vigneshwar, > > the problem is fixed now in the release-4-0-patches branch. > > Carsten > > > On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: > > > Hi, > > > > apparently this bug fix made it to 4.5, bu

Re: [gmx-users] segmentation fault: g_velacc

Hi Vigneshwar, the problem is fixed now in the release-4-0-patches branch. Carsten On Feb 1, 2011, at 2:00 PM, Carsten Kutzner wrote: > Hi, > > apparently this bug fix made it to 4.5, but not to 4.0. > I will apply the fix also there. > > Carsten > > On Feb 1, 2011, at 1:58 PM, Justin A.

Re: [gmx-users] segmentation fault: g_velacc

Hi, apparently this bug fix made it to 4.5, but not to 4.0. I will apply the fix also there. Carsten On Feb 1, 2011, at 1:58 PM, Justin A. Lemkul wrote: > > > Vigneshwar Ramakrishnan wrote: >> Dear All, >> I am using the gromacs 4.0.7 version and I was trying to calculate the >> momentum aut

Re: [gmx-users] segmentation fault: g_velacc

Vigneshwar Ramakrishnan wrote: Dear All, I am using the gromacs 4.0.7 version and I was trying to calculate the momentum autocorrelation function by using the -m flag. However, I get a segmentation fault as follows: trn version: GMX_trn_file (double precision) Reading frame 0 time

Re: [gmx-users] segmentation fault while running eneconv

Anna Marabotti wrote: Dear all, I launched on my system a first simulation of 5 ns, then I prolonged it to 50 ns using tpbconv -s tpr1_5ns.tpr -until 5 -o tpr2_50ns.tpr and then mdrun -s tpr2_50ns.tpr -deffnm md2_50ns -cpi md1_5ns.cpt Since my simulation was interrupted several times, e

Re: [gmx-users] Segmentation Fault in EM

TJ Mustard wrote: On January 17, 2011 at 1:20 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > Hi all, > > > > > > > > I have been running alot of simulations on protein ligand interactions, > > and my settings/setup/mdp files worked great for one system. Th

Re: [gmx-users] Segmentation Fault in EM

  On January 17, 2011 at 1:20 PM "Justin A. Lemkul" wrote: > > > TJ Mustard wrote: > > > > > > Hi all, > > > >  > > > > I have been running alot of simulations on protein ligand interactions, > > and

Re: [gmx-users] Segmentation Fault in EM

TJ Mustard wrote: Hi all, I have been running alot of simulations on protein ligand interactions, and my settings/setup/mdp files worked great for one system. Then when we moved to a larger and more complicated system we started getting mdrun segmentation faults during "steep" energy m

Re: [gmx-users] segmentation fault

I managed to run my simulation but which kind of coulomtype can I use except PME? also I get different averages for kinetic and potential energies than before reducing units I think these numbers must be the same because E*=E/epsilon (epsilon is about 0.9977) for argon. could u please help me about

Re: [gmx-users] segmentation fault

On 15/01/2011 8:50 PM, leila separdar wrote: I have Gromacs 4.0.7 I have simulated 1000 atoms of Argon with Lenard Jones potential in a cubic box with linear size of 3.34. but when I reduced units I confront with this error Back Off! I just backed up md.log to ./#md.log.5# Reading file argon.tp

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund wrote: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fa

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 21.15: leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 16.52: Dear Erik there are several hb->per->pHist in gmx_hbond.c. please say me exactly in which part of the gmx_hbond.c file if-statement should be placed? If I install gromacs 4.5.2 or 4.5.3, is there not this problem (segmentation fault)? -- Leila Karami

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 16.36: Erik Marklund skrev 2010-12-18 16.23: leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistr

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 16.23: leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group I can reproduce the segfault.

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 16.18: Dear Erik excuse me, I sent .xtc and .tpr file your e-mail. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group I can reproduce the segfault. It doesn't happen without -hbn. I'll ha

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 15.40: leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 15.38: Dear Erik thanks for your attention. in version 4.5.1, when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn, gromacs give me only hbnum.xvg with segmentation fault. when I use g_hbond -f .xtc -s .tpr -n .ndx -num -g, gromacs give me only hbnum.xvg witho

Re: [gmx-users] Segmentation fault in g_hbond

Erik Marklund skrev 2010-12-18 15.02: leila karami skrev 2010-12-18 14.50: Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group Interesting. Could you file a

Re: [gmx-users] Segmentation fault in g_hbond

leila karami skrev 2010-12-18 14.50: Dear Erik I used g_hbond in 4.5.1 but problem was not solved. -- Leila Karami Ph.D. student of Physical Chemistry K.N. Toosi University of Technology Theoretical Physical Chemistry Group Interesting. Could you file a bugzilla and attach a tpr and xtc/trr

Re: [gmx-users] Segmentation fault in g_hbond

Hi, Upgrade to 4.5.x and see if the problem persists. I've hacked g_hbond quite a bit since 4.0.5. Erik leila karami skrev 2010-12-18 14.02: Dear gromacs users I'm using gromacs 4.0.5. with following command: g_hbond -f .xtc -s .tpr -n .ndx -num -g -hbn. my system contains protein, dna an

Re: [gmx-users] Segmentation fault at g_traj

Jorge Alberto Jover Galtier wrote: Dear friends: Running several simulations, we have found a problem with the 'g_traj' utility. It doesn't finish properly the files it generates, and gives a segmentation fault. This is what we have done: We are working with double precision. With the file

Re: [gmx-users] Segmentation fault with gromacs executables

On 26/04/2010 3:44 PM, Mark Abraham wrote: On 26/04/2010 2:45 PM, Sikandar Mashayak wrote: Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without spe

Re: [gmx-users] Segmentation fault with gromacs executables

On 26/04/2010 2:45 PM, Sikandar Mashayak wrote: Hi I am facing this strange problem of segmentation fault while executing mpi-enabled gromacs executables on remote server. I source GMXRC, so that I can access executables from any directory without specifying full path of gromacs/bin. And when I

Re: [gmx-users] segmentation fault in position restrained step

Moeed wrote: Dear Justin, 1- Could you please check if I have grouped atoms properly? Lastly, I could generate the tpr file for PR step. Since I am getting segmentation fault in the next step I though maybe there is sth wring with charge groups.. I don't know how your labeling is set up.

Re: [gmx-users] Segmentation fault with g_order

Javier Cerezo wrote: Hello I tried to run g_order on a cluster with Core 2 Quad Q6600 processor where the Gromacs Suite 4.0.1 has been compiled in single precision. The program stops with a message from the compiler (i.e. in Spanish): "Violación de segmento" (=Segmentation fault, I guess) a

Re: [gmx-users] segmentation fault with grompp

I just used this topology in conjunction with popc128a.pdb (with some naming adjustments to match the topologies), and everything worked fine. I am using version 4.0.5, as well. Are you running grompp on a local workstation, or on a remote filesystem? I have noticed sporadic, unpredictable

Re: [gmx-users] segmentation fault with grompp

Gard Nelson wrote: Hey everyone, I wrote a few days ago about a segmentation fault I'm getting from grompp when I try to set up a membrane protein system. Grompp opens the ff_dum.itp file and then the core dumps immediately. This happens on two different machines, both of which are running

Re: [gmx-users] segmentation fault with grompp

Gard Nelson wrote: Hi all, I'm trying to simulate a solvated membrane using Berger's lipids. When I run grompp, i get the following error: checking input for internal consistency... processing topology... Opening library file ...lipid.itp Opening library file ...nb_lipid.itp Opening library

Re: [gmx-users] Segmentation fault (11)

Ricardo O. S. Soares wrote: Hi everyone, could anyone help me with this? I already searched the mailing archives, with no luck. I just installed gromacs 4.0.7 in a new computer here, same as always (with mpi support), but now I get this error whem I run MDRUN with or without mpirun (openm

Re: [gmx-users] Segmentation fault when using fourier dihedrals in v. 4.0.5.

On Tue, Dec 1, 2009 at 11:22, Henri Ervasti wrote: > I just upgraded from Gromacs 4.0.2 to 4.0.5. I wanted to re-run some > jobs from the previous version to see if there would be any changes in > results. I have systems with Ryckaert-Bellemans (type 3) dihedrals and > Fourier (type 5) dihedrals.

RE: [gmx-users] segmentation fault in g_anaeig

Hi, The problem that I fixed last week occured after the use of g_covar -mwa with a fit selection that is not the first N atoms of the system. Berk > Date: Tue, 17 Nov 2009 18:03:37 +0100 > Subject: Re: [gmx-users] segmentation fault in g_anaeig > From: tsje...@gmail.com > T

Re: [gmx-users] segmentation fault in g_anaeig

Hi Nilu, Can you paste the exact commands you entered, and indicate the selections you made? Oh, and can you check the archives to whether this is the same problem that was reported a few weeks ago? Cheers, Tsjerk On Tue, Nov 17, 2009 at 5:53 PM, Nilu Chakrabarti wrote: > I am used to do PC an

Re: [gmx-users] Segmentation fault while running MD simulation

rainy...@yahoo.com wrote: Hi Amit, My system is quite large, comprising of a molecule, water, and Na+ ions, summing up to 233863 (!) entities total. Regarding the segmentation fault, the MD simulation only ran for 2 steps before the system crashed. 2 steps? Your original post with ver

Re: [gmx-users] Segmentation fault while running MD simulation

Hi Amit, My system is quite large, comprising of a molecule, water, and Na+ ions, summing up to 233863 (!) entities total. Regarding the segmentation fault, the MD simulation only ran for 2 steps before the system crashed. Could the size of my system caused it to crash? Also, in my md.log file

Re: [gmx-users] Segmentation fault while running MD simulation

hi, could you specify the system size? How many steps did it run before you got the segmentation fault? Try to find if everything went ok until the segmentation fault by saving log and trajectories. amit On Fri, Nov 13, 2009 at 3:53 PM, Justin A. Lemkul wrote: > > > rainy...@yahoo.com wrote

Re: [gmx-users] Segmentation fault while running MD simulation

rainy...@yahoo.com wrote: Hi, The relevant lines of my script are the following: line 27: # Run MD and write output to /nas2 disk line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr line 29: line 30: # MDRUN completes:

Re: [gmx-users] Segmentation fault while running MD simulation

rainy...@yahoo.com wrote: Hi Justin, Sorry I didn't include all of my md.mdp file, as it is quite long :). I have included as a reference below. I've taken a look at the log file, but I'm not really sure what I should be looking for so to identify what is causing my system to blow up? Sh

Re: [gmx-users] Segmentation fault while running MD simulation

Hi, The relevant lines of my script are the following: line 27: # Run MD and write output to /nas2 disk line 28: $MDRUN -v -nice 0 -np $NSLOTS -s npg3_4.tpr -o npg3_4.trr -c confout.gro -g npg3_4.log -x npg3_4.xtc -e npg3_4.edr line 29: line 30: # MDRUN completes: now make the next run file for a

Re: [gmx-users] Segmentation fault while running MD simulation

Hi Justin, Sorry I didn't include all of my md.mdp file, as it is quite long :). I have included as a reference below. I've taken a look at the log file, but I'm not really sure what I should be looking for so to identify what is causing my system to blow up? Should I start with the energies (s

Re: [gmx-users] Segmentation fault while running MD simulation

rainy...@yahoo.com wrote: Hi all, I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy minimization. I tried to run the inital MD simulation, but the job was cut short due to a segmentation fault, as mentioned in the

Re: [gmx-users] Segmentation fault while running MD simulation

rainy...@yahoo.com wrote: Hi all, I've encountered a problem while trying to run Gromacs on my coarse-grained molecule. I've already performed the initial energy minimization. I tried to run the inital MD simulation, but the job was cut short due to a segmentation fault, as mentioned in t

RE: [gmx-users] Segmentation Fault (Address not mapped)

> You indicate that I need to read the primary literature for the force > fields. Could you please tell me where this literature can be found? I > have searched using Google for the forcefields available for use in > GROMACS (G43b1, G43a1, G43a2, G45a3, G53a5, G53a6, gmx), but have not > found any

Re: [gmx-users] Segmentation Fault (Address not mapped)

-Justin Thanks again. Darrell Date: Tue, 04 Aug 2009 12:14:07 +1000 From: Mark Abraham Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a77996f.9070...@anu.edu.au> Content-Type: text/plain; charset=windows-1252; forma

Re: [gmx-users] Segmentation Fault (Address not mapped)

you very much for your assistance. Darrell Date: Mon, 27 Jul 2009 17:48:02 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a6e2092@vt.edu> Content-Type: text/plain; charset=wi

RE: [gmx-users] Segmentation Fault (Address not mapped)

> And, by the way, I have resolved the segmentation fault problem. It was > being caused by the freezing of the graphene lattice. When I removed > the > freezing, I saw the graphene structure curl upward and am thinking that > by freezing the atoms in place it was creating great forces between the

Re: [gmx-users] Segmentation Fault (Address not mapped)

the values you think you are. -Justin Thanks again for your help. Darrell >Date: Fri, 17 Jul 2009 22:11:07 -0400 >From: "Justin A. Lemkul" >Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) >To: Discussion list for GROMACS users >Mess

Re: [gmx-users] Segmentation Fault (Address not mapped)

omething is going to go careening off into infinity. -Justin Thanks again for your help. Darrell Date: Fri, 17 Jul 2009 19:08:38 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a61047

Re: [gmx-users] Segmentation Fault (Address not mapped)

nks again for your help. Darrell Date: Thu, 16 Jul 2009 16:20:04 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a5f8b74.6070...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1

Re: [gmx-users] Segmentation Fault (Address not mapped)

ain for your help. Darrell Date: Thu, 16 Jul 2009 07:15:12 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a5f0bc0.4020...@vt.edu> Content-Type: text/plain; charset=ISO-8859-1;

Re: [gmx-users] Segmentation Fault (Address not mapped)

rk Abraham Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a5e6aa5.4040...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrote: Hi Mark, Yes, I know that the box dimensions ar

Re: [gmx-users] Segmentation Fault (Address not mapped)

ation) Can you post a corrected and current .mdp file? Mark Date: Wed, 15 Jul 2009 16:59:21 +1000 From: Mark Abraham Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a5d7e49.9020...@anu.edu.au> Content-Type: text/plain; chars

Re: [gmx-users] Segmentation Fault (Address not mapped)

gy =500 nstlist =500 Please let me know what you think might be the problem. Thank you very much. Darrell Date: Mon, 13 Jul 2009 15:37:15 -0400 From: "Justin A. Lemkul" Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GR

Re: [gmx-users] Segmentation Fault (Address not mapped)

Date: Tue, 07 Jul 2009 09:19:42 +1000 From: Mark Abraham Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a52868e.6010...@anu.edu.au> Content-Type: text/plain; charset=ISO-8859-1; format=flowed darre...@ece.ubc.ca wrot

Re: [gmx-users] Segmentation Fault (Address not mapped)

probably the gro file does not match the trr file (more atoms in trr than in gro). Thanks. Darrell Date: Tue, 07 Jul 2009 09:19:42 +1000 From: Mark Abraham Subject: Re: [gmx-users] Segmentation Fault (Address not mapped) To: Discussion list for GROMACS users Message-ID: <4a52868e.6

Re: [gmx-users] Segmentation Fault (Address not mapped)

a layer of ammonia molecules above it. The box is very large and there is lots of empty space in the box. So I am a little confused as to how the box could be exploding. Thanks again in advance for your help. Darrell Koskinen Date: Fri, 03 Jul 2009 11:41:45 +1000 From: Mark Abraham Subject: Re:

Re: [gmx-users] Segmentation Fault (Address not mapped)

darre...@ece.ubc.ca wrote: Dear GROMACS Gurus, I am experiencing a segmentation fault when mdrun executes. My simulation has a graphene lattice with an array (layer) of ammonia molecules above it. The box is three times the width of the graphene lattice, three times the length of the graphene lat

Re: [gmx-users] Segmentation fault

Chih-Ying Lin wrote: Hi I run the simulation on MPI. first, i make constraints=all bond => successful second, i make constraints=none => segmentation fault is the "segmentation fault" coming from the NONE bond-contraints? The rest of your parameters and whatever is in your system is no

Re: [gmx-users] segmentation fault - extending trajectory uwing gmx4.0.4 on 16 processors with PME

Ángel Piñeiro wrote: Dear all, I have some membrane protein systems running in our cluster using gmx4.0.4. The minimizations finish with reasonable potential energy values (of the order of 10^-5 with maximum forces of the order of 10^-3). Then I am trying to run several 1-ns-long equilibration MD

Re: [gmx-users] segmentation fault after mdrun

Nikit sharan wrote: Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the Try an even number. accuracy.But then the simulation is not getting completed.Its taking hours together.Normally what's the r

Re: [gmx-users] segmentation fault after mdrun

On Feb 23, 2009, at 9:22 AM, Nikit sharan wrote: Dear justin, As you suggested i have changed the coloumb type to PME and set pme_order to 5 as said in the mailing list as it will increase the Hi Nikit, I think pme_order should be an even number in gromacs. You might want to try with order =

  1   2   >