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

On 4/28/20 5:08 AM, Elham Taghikhani wrote: Hi As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom. And the atom

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

Hi As you said I checked my structure for any bad contact, but the close atoms are part of the protein so I can't delete them to minimize the structure. And water molecules are not that much close to make bad contact with the atom. And the atom which errored during minimization it's the atom

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

On 4/19/20 4:38 PM, Elham Taghikhani wrote: Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? Calculate interatomic distances and look for

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

Thank you I corrected the mdp file. As you said I opened my gro file in VMD but I didn't notice any bad contact around the atom. Could you explain how can I observe bad contacts in the structure? I even tried the different box size but it didn't work. Both ligand and protein are ok with

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

On 4/19/20 2:43 PM, Elham Taghikhani wrote: Hi  I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents:    Tolerance (Fmax)   =  1.0e+03    Number of steps    =    5 Step=    0, Dmax= 1.0e-02 nm, Epot= 

[gmx-users] Segmentation fault (core dumped) error during minimization

Hi  I am simulating a protein-ligand system, using oplss force field but i got this error during minimization. Steepest Descents:    Tolerance (Fmax)   =  1.0e+03    Number of steps    =    5 Step=    0, Dmax= 1.0e-02 nm, Epot=  1.27151e+33 Fmax= 4.76291e+07, atom= 1996 Segmentation

Re: [gmx-users] segmentation fault gmx do_dssp

On 4/10/20 8:07 PM, Sadaf Rani wrote: Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Your version should be fine, but make sure the dssp binary works properly on its own

Re: [gmx-users] segmentation fault gmx do_dssp

Dear Justin and Qinghua I am using gromacs 2020 for analysis and dssp version on my system is 2.2.1. Which version of dssp would be compatible with gromacs 2020? Qinghua, I am already using the stripped trajectory. Any suggestions would be appreciated. Thanks. Sadaf -- Gromacs Users mailing

Re: [gmx-users] segmentation fault gmx do_dssp

On 4/10/20 5:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading

Re: [gmx-users] segmentation fault gmx do_dssp

Hello, I guess the problem is about memory. You could strip the water and ions first, then process the striped trajectory. All the best, Qinghua On 4/10/20 11:48 PM, Sadaf Rani wrote: Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to

[gmx-users] segmentation fault gmx do_dssp

Dear Gromacs users I am doing an analysis of protein-ligand MD simulation of 150ns. I am trying to calculate secondary structure as below:- gmx do_dssp -f md_noPBC.xtc -s md.tpr -o ss.xpm -tu ns -dt 1 But I am getting segmentation fault error. Reading file md.tpr, VERSION 2020-UNCHECKED (single

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

Hi, gmx solvate shouldn't segfault based on a minor change to the input coordinates, so it's probably a bug to look into. Please open an issue at https://redmine.gromacs.org and attach inputs with a failing gmx command, and someone can likely provide some insight! Mark On Thu, 14 Nov 2019 at

[gmx-users] Segmentation fault using gmx solvent

Hi all, I've been fighting a particularly painful problem with a system I'm building in Gromacs. gmx mdrun (grompp worked on the system) has been throwing a segmentation fault on my collagen system in a vacuum. Shortly after, I tried gmx solvate but that too was also throwing a segmentation

Re: [gmx-users] segmentation fault core dumped

On 11/14/19 6:17 AM, Yogesh Sharma wrote: Greetings everyone I was following protein ligand complex tutorial. Given the atom names listed below, you're not doing the tutorial but perhaps are trying to follow its method? There's a big difference. If you're doing something different, you

Re: [gmx-users] segmentation fault core dumped

First of all optimize the geometry of protein by using wincoot especially considering your respective atom/molecule/amino acid Change the algorithm of energy minimization to conjugate gradient If you can see the respective atom it is in collision with any other atom in any visualization tool. This

[gmx-users] segmentation fault core dumped

Greetings everyone I was following protein ligand complex tutorial. EM run was fine even with double precision. Steepest Descents converged to Fmax < 1000 in 101 steps Potential Energy = -2.71399964872904e+06 Maximum force = 9.15885947946535e+02 on atom 4411 Norm of force =

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

oms) > > Found 13 donors and 25 acceptors > > trr version: GMX_trn_file (single precision) > > Reading frame 0 time0.000 > > Will do grid-seach on 2374x2374x2374 grid, rcut=0.35 > > Segmentation fault (core dumped) > > ____

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

n (130 atoms) >> >> Found 13 donors and 25 acceptors >> >> trr version: GMX_trn_file (single precision) >> >> Reading frame 0 time0.000 >> >> Will do grid-seach on 2374x2374x2374 grid, rcut=0.35 >> >> Segmentation fault (core dumped) >>

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

Hi Najamuddin, > > I tried xtc file instead of trr, still same error shows up. > > Thank you, > Neena > > > From: Neena Susan Eappen > Sent: Wednesday, May 29, 2019 5:25 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject:

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

Eappen Sent: Wednesday, May 29, 2019 5:25 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Segmentation fault, core dumped error Command: gmx hbond -f md_0_1.trr -s md_0_1.tpr Specify 2 groups to analyze: Group 0 (System) has 130 elements Group 1 (Protein) has

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

) > > ____ > From: Neena Susan Eappen > Sent: Tuesday, May 28, 2019 11:31 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Segmentation fault, core dumped error > > Hello gromacs users, > > Is there a reason why

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

) From: Neena Susan Eappen Sent: Tuesday, May 28, 2019 11:31 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: Re: [gmx-users] Segmentation fault, core dumped error Hello gromacs users, Is there a reason why segmentation fault appeared when gmx hbond command was used? Thank you, Neena

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

appeared when gmx hbond command was used? Thank you, Neena From: Neena Susan Eappen Sent: Friday, May 24, 2019 12:40 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Segmentation fault, core dumped error Hello gromacs users, I got an error

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

a reason why segmentation fault appeared when gmx hbond command was > used? > > Thank you, > Neena > > > From: Neena Susan Eappen > Sent: Friday, May 24, 2019 12:40 PM > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Segme

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

Hello gromacs users, Is there a reason why segmentation fault appeared when gmx hbond command was used? Thank you, Neena From: Neena Susan Eappen Sent: Friday, May 24, 2019 12:40 PM To: gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users] Segmentation

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

http://www.gromacs.org/Documentation/Terminology/Blowing_Up On Tue, 18 Sep. 2018, 3:14 pm Ashma Khan, wrote: > when I run gmx mdrun -v -deffnm 5e61_pr for pr.mdp file then there is an > error of core dumped.Please suggest what should I do > > Step 7, time 0.014 (ps) LINCS WARNING > relative

[gmx-users] Segmentation fault (core dumped)

when I run gmx mdrun -v -deffnm 5e61_pr for pr.mdp file then there is an error of core dumped.Please suggest what should I do Step 7, time 0.014 (ps) LINCS WARNING relative constraint deviation after LINCS: rms 0.041436, max 2.491113 (between atoms 3683 and 3684) bonds that rotated more than 30

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

Please pest the entire error lines in this mailing list. It may possible due to lack of proper minimization of your starting coordinates. On Mon, Sep 10, 2018, 11:22 AM Ashma khan wrote: > When I am running the gmx mdrun -v -deffnm 5e61_nvt there is an error of > core dumped.I have increased

[gmx-users] Segmentation fault (core dumped)

When I am running the gmx mdrun -v -deffnm 5e61_nvt there is an error of core dumped.I have increased the equilibration time but the same error has occured.So,please suggest me what should I do -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] segmentation fault (core?==?utf-8?q? dumped) error with gmx confrms

Hi, On Tue, Jul 31, 2018 at 5:08 PM Jahn Nitschke wrote: > Dear community, > > i have a segmentation fault (core dumped) error with gmx confrms. > In more detail: i extracted the average structure of four different > ligands with the same backbone from a solvent simulation and wanted to use >

[gmx-users] segmentation fault (core?==?utf-8?q? dumped) error with gmx confrms

Dear community, i have a segmentation fault (core dumped) error with gmx confrms. In more detail: i extracted the average structure of four different ligands with the same backbone from a solvent simulation and wanted to use confrms to calculate the rmsd between the backbone. This works. I

[gmx-users] Segmentation fault and PCA Analysis

Dear users, I am trying to align my trajectory to an average structure pdb, the problem is that I have "Segmentation fault (core dumped)" while taking this pdb as a reference structure, while it worked with the em.tpr file ... I also tried to extract the pdb from the that em.tpr using gmx

Re: [gmx-users] segmentation fault

On 3/7/18 6:11 AM, sp...@iacs.res.in wrote: Hii all I am trying to simulate biomolecule in Guanidinium chloride in AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in energy minimization step but in NVT

[gmx-users] segmentation fault

Hii all I am trying to simulate biomolecule in Guanidinium chloride in AMBER99sb-ildn force field. I have prepared the topology of GdmCl taking the parameters from ffbonded.itp and ffnonbonded.itp. It goes well in energy minimization step but in NVT step files are generated and shows segmentation

Re: [gmx-users] segmentation fault for unknown reason

On 8/2/17 3:23 PM, gangotri dey wrote: Hello! I am trying to minimize a periodic MnO2 surface using UFF force fields. I have previously computed many structures using MnO2 clusters. I did not face much problem. However, when I am trying to compute the minimization using the following

[gmx-users] segmentation fault for unknown reason

Hello! I am trying to minimize a periodic MnO2 surface using UFF force fields. I have previously computed many structures using MnO2 clusters. I did not face much problem. However, when I am trying to compute the minimization using the following minim.mdp there is segmentation error as follows.

[gmx-users] Segmentation fault (core dumped) Too many LINCS warnings

​Dear All I've been trying to create a DPPC bilayer with polarizable water for the past week, but I've gotten "Segmentation fault (core dumped)" error message every single time during the production run, and despite all my efforts, I haven't been able to figure out a solution for this error. My

Re: [gmx-users] segmentation fault in gmx hbond

Dear Dr Justin, Thank you for your message. I installed gromacs 2016.2 version and found that it gives no error while using -ac option in gmx hbond analysis tool. Now, I could able to do the calculations without any trouble. Thank you all again, With Best Regards, Dr Dilip H Dagade, Department

Re: [gmx-users] segmentation fault in gmx hbond

On 3/1/17 6:17 AM, Dr. D. H. Dagade wrote: Dear Prof David van der Spoel and all others, Thank you very much for the reply. I will wait for the release of GROMACS 2016.2 version. Could the version 2016.2 will be used to analyse the It was released last month:

Re: [gmx-users] segmentation fault in gmx hbond

ologies for DHF/NADPH (Nicolas Cheron) >5. Re: PDB2GMX Fatal Error (Syed Azeem) > > > -- > > Message: 1 > Date: Wed, 1 Mar 2017 12:30:24 +0530 > From: Tasneem Kausar <tasneemkausa...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] segmentation fault in gmx hbond > Message-ID: >

Re: [gmx-users] segmentation fault in gmx hbond

On 01/03/17 07:51, Dr. D. H. Dagade wrote: Dear Gromacs users, I am doing hbond analysis of various organic anions after doing successful free energy calculations with timestep of 2fs using GROMACS 2016.1 version. While using -ac option for autocorrelation, I got following error.

[gmx-users] segmentation fault in gmx hbond

Dear Gromacs users, I am doing hbond analysis of various organic anions after doing successful free energy calculations with timestep of 2fs using GROMACS 2016.1 version. While using -ac option for autocorrelation, I got following error. Doing autocorrelation according to the theory of

[gmx-users] Segmentation Fault

Hello everyone,I am using FF:53a6spc watermodelgromacs verion 5.0.7 I am currently simulating heme containing protein and I get segmentation error in equilibration step. What should I do? I read on discussion forum that the reason behind this, forces may be too high or may have enormous positive

Re: [gmx-users] Segmentation fault in MDRUN

You may try with dt = 0.001. Also maybe you can increase the equilibration time. On 25 Jan 2017, at 09:30, Matteo Busato wrote: > > dt = 0.002 -- Gromacs Users mailing list * Please search the archive at

[gmx-users] Segmentation fault in MDRUN

Goodmorning, I am trying to perform a very simple dynamic of an atom of Cu2+ in a box of tip3p water using the OPLS force field on GROMACS 5.0.4. I have done an energy minimization using the steepest algorythm and equilibrations in NVT and NPT ensemble, but during the mdrun of the dynamics I

Re: [gmx-users] Segmentation fault error during run

On 1/18/17 4:57 AM, Yasser Almeida Hernández wrote: Hi all, I am simulating a solvated system with a membrane protein and detergent NG (beta-nonylgrucoside), using GROMACS 4.6.5. I got the topology for NG from ATB database. During the simulation I got this Segmentation fault error:

[gmx-users] Segmentation fault error during run

Hi all, I am simulating a solvated system with a membrane protein and detergent NG (beta-nonylgrucoside), using GROMACS 4.6.5. I got the topology for NG from ATB database. During the simulation I got this Segmentation fault error: (...) Step 173550, time 347.1 (ps) LINCS

Re: [gmx-users] segmentation fault with unusually high temperature and energy values

On 10/5/16 6:12 AM, Sahithya S Iyer wrote: Hi gmx users, I am trying to set up a membrane protein system. The protein has to be at a specific location of the heterogeneous bilayer patch (hence i cannot use inflateGRO.py) to set up the system. I used vmd to place the protein and remove

Re: [gmx-users] segmentation fault in md

On 10/3/16 2:38 AM, ISHRAT JAHAN wrote: Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am pasting my em.mdp and pr.mdp file below- em.mdp ; ;User spoel (236) ;Wed Nov 3

[gmx-users] segmentation fault in md

Dear all I am trying to simulate 3M urea in a water box.when i do the mdrun of pr , i get too many LINCS warning and also segmentation fault(core dumped). I am pasting my em.mdp and pr.mdp file below- em.mdp ; ;User spoel (236) ;Wed Nov 3 17:12:44 1993 ;Input file ; cpp

Re: [gmx-users] Segmentation fault

Please make sure to use a proper subject line and do not reply to the entire digest. On 8/29/16 6:16 AM, Seera Suryanarayana wrote: Sub: Segmentation fault Dear Justin and Vivek, I came to know what was my fault. I added the refcoordscale = com in .mdp file and it going fine. I have

Re: [gmx-users] Segmentation fault

On 8/27/16 5:32 PM, vivek naik wrote: I don't think you can do a simulation with pressure if you have position restraints, except if your restrained atoms are all in the same plane. This is not true. However, ref_coordscaling option should be 'com', which should make it better than it is

Re: [gmx-users] Segmentation fault

On 8/27/16 2:45 AM, Seera Suryanarayana wrote: Dear gromacs users, I have done mdrun for 10ns with position restrain of interest of our residues. Here I woulk like to explain how I did the position restrain. During gmx pdb2gmx command we usually get posre.itp file which we use in the

Re: [gmx-users] Segmentation fault

I don't think you can do a simulation with pressure if you have position restraints, except if your restrained atoms are all in the same plane. However, ref_coordscaling option should be 'com', which should make it better than it is now. Also, there is no way isotropic pressure is going to work.

[gmx-users] Segmentation fault

Dear gromacs users, I have done mdrun for 10ns with position restrain of interest of our residues. Here I woulk like to explain how I did the position restrain. During gmx pdb2gmx command we usually get posre.itp file which we use in the equilibrium process to restraint the protein. As I want to

Re: [gmx-users] SEGMENTATION FAULT (Core dumped)

On 6/28/16 2:57 AM, Luca Banetta wrote: I try to launch the simulation with the line you wrote me Justin, but unfortunately this fatal error appears: Setting the total number of threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI I worked on a HPC that is

Re: [gmx-users] SEGMENTATION FAULT (Core dumped)

I try to launch the simulation with the line you wrote me Justin, but unfortunately this fatal error appears: Setting the total number of threads is only supported with thread-MPI and Gromacs was compiled without thread-MPI I worked on a HPC that is managed by another department in my

Re: [gmx-users] SEGMENTATION FAULT (Core dumped)

Ok. So do i try with PD, particle decomposition? Il 27/Giu/2016 16:41, "Justin Lemkul" ha scritto: > > > On 6/27/16 10:35 AM, Luca Banetta wrote: > >> Dear gromacs users, >> I currently work on a project about a polarizable model of acetone >> molecule. >> Unfortunately the

Re: [gmx-users] SEGMENTATION FAULT (Core dumped)

On 6/27/16 10:35 AM, Luca Banetta wrote: Dear gromacs users, I currently work on a project about a polarizable model of acetone molecule. Unfortunately the simulations work using only 1 MPI thread. When we attempt to parallelize it this error appears: [compute-0-4:21947] *** Process received

[gmx-users] SEGMENTATION FAULT (Core dumped)

Dear gromacs users, I currently work on a project about a polarizable model of acetone molecule. Unfortunately the simulations work using only 1 MPI thread. When we attempt to parallelize it this error appears: [compute-0-4:21947] *** Process received signal *** [compute-0-4:21947] Signal:

Re: [gmx-users] Segmentation Fault - Water on Substrate

>From: Mark Abraham <mark.j.abra...@gmail.com> >To: gmx-us...@gromacs.org, "gromacs.org_gmx-users@maillist.sys.kth.se" > <gromacs.org_gmx-users@maillist.sys.kth.se> >Subject: Re: [gmx-users] Segmentation Fault - Water on Substrate >Message-ID: >

Re: [gmx-users] Segmentation Fault - Water on Substrate

Hi, You're presumably making one of your formerly periodic dimensions differently periodic when you combine your boxes. If your input structure has molecules with coordinates that are broken across the former boundary, you need to make them whole before your merge can work sanely. Mark On Sun,

[gmx-users] Segmentation Fault - Water on Substrate

Dear Gromacs users, I am want to simulate water on a substrate. I have a water.pdb file with the coordinates of a cuboid of water and a substrate.pdb file with the coordinates of the substrate. The box dimensions along the x and y directions are identical for both files. I run two simulations

Re: [gmx-users] Segmentation fault after merging two equilibrated molecules!

ussion list for GROMACS users <gmx-us...@gromacs.org> Subject: Re: [gmx-users] Segmentation fault after merging two equilibrated molecules! Hi Sajjad, maybe a periodic boundary issue (they seem to be apart in the central simulation box, but are superimposed with the periodic images o

Re: [gmx-users] Segmentation fault after merging two equilibrated molecules!

Hi Sajjad, maybe a periodic boundary issue (they seem to be apart in the central simulation box, but are superimposed with the periodic images of each other)? try to open the structure with a program that allows periodic images to be visualized along with the central box to see if there are any

[gmx-users] Segmentation fault after merging two equilibrated molecules!

Dear experts, I want to simulate a system with a cnt and a molecule passing through it by a coarse grained ff. First, I ran a nvt (after an em) for a single molecule (no solvent) with no problem. Second, I do the same with a single cnt and absolutely no problem. The problem is where I put them

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsapolar energy calculation

Hi, There's a good clue of who to contact in the copyright statement and the website you downloaded the code from :-) This tool is not part of official GROMACS. Mark On Thu, Jun 2, 2016 at 6:57 AM Nikhil Maroli wrote: > All the best!! > > -- > Gromacs Users mailing list >

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsapolar energy calculation

All the best!! -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsa polar energy calculation

gt; > -- > > Message: 1 > Date: Wed, 1 Jun 2016 08:49:23 +0000 (UTC) > From: Nikhil Maroli <scinik...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Segmentation Fa

[gmx-users] Segmentation Fault (core dumped) in g_mmpbsa

#source can someone please help me to solve this problem? Justin sir? Date: Wed, 1 Jun 2016 08:49:23 + (UTC) > From: Nikhil Maroli <scinik...@gmail.com> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: Re: [gmx-users] Segmentation Fault (core dumped) in >

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsapolar energy calculation

Please see the previous mailing list,this problem normally occurs incompatible APBS and g_mmpbsa check your installation carefully -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] Segmentation Fault (core dumped) in g_mmpbsa polar energy calculation

Hi, You can probe for memory issues by running subsets of your original calculation, e.g. fewer trajectory frames (or however g_mmpbsa works). Mark On Wed, Jun 1, 2016 at 10:16 AM Pavithra wrote: > Dear users, > > I have installed g_mmpbsa package for MMPBSA

Re: [gmx-users] Segmentation fault during equilibration

Hi, As normal, even for coarse-grained simulations, equilibration may require bigger rearrangements for some starting conditions than others. The usual advice for http://www.gromacs.org/Documentation/Terminology/Blowing_Up still applies - particularly to try smaller time steps while relaxing what

[gmx-users] Segmentation fault during equilibration

Hi all, I am running an equilibration of a membrane/protein coarse grained system and got this Segmentation fault error. --- Reading file equilibration.protein_DPPC.tpr, VERSION 4.6.5 (single precision) Using 8 MPI threads Compiled acceleration: SSE4.1 (Gromacs could use AVX_256 on this

Re: [gmx-users] Segmentation fault while using external water model

Hi, I’m not entirely sure. How can I check? Below is my .mdp file (with misleading/old comments): title = OPLS Lysozyme NVT equilibration define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md; leap-frog integrator nsteps

Re: [gmx-users] Segmentation fault while using external water model

Hi, Are these bonds being converted to constraints, like the original message suggested? Mark On Fri, 19 Feb 2016 02:14 Irem Altan wrote: > Hi, > > I am still having trouble using TIP4P2005. When I start running my MD > simulation, it “runs” for a minute or so (although

[gmx-users] Segmentation fault while using external water model

Hi, I am still having trouble using TIP4P2005. When I start running my MD simulation, it “runs” for a minute or so (although it does not start the simulation itself), and then crashes with a segmentation fault. I have (modified) copy of the amber99sb forcefields in my working directory, and I

[gmx-users] Segmentation fault (core dumped) after grompp minimization

Hello, i'm working with a 256 phospholipid membrane and i run grompp for minimization and to generate a .tpr file, so after run grompp i run the mdrun but instantly crushed with the legend: SSteepest Descents: Tolerance Fmax: 1.e03. No. of steps: 50,000, nan Fmax: inf, atom: 30983.

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

On 2/5/16 1:07 PM, Poncho Arvayo Zatarain wrote: Hello, i'm working with a 256 phospholipid membrane and i run grompp for minimization and to generate a .tpr file, so after run grompp i run the mdrun but instantly crushed with the legend: SSteepest Descents: Tolerance Fmax: 1.e03. No.

Re: [gmx-users] segmentation fault with GPU

Hi, You need to start by looking at your log file and terminal output. Mark On Sat, Nov 21, 2015 at 12:46 PM xiao wrote: > Dear GMX uses, > I got an error " segmentation fault (core dumped)" while i was doing a NVT > equilibrium simulation, the error disappeared when GPU is

[gmx-users] segmentation fault with GPU

Dear GMX uses, I got an error " segmentation fault (core dumped)" while i was doing a NVT equilibrium simulation, the error disappeared when GPU is disabled with -nb cpu. The GMX version is gromacs-5.1.1. The GPU is: GTX980 The GMX was compiled by the following command: cmake .. -DGMX_GPU=ON

[gmx-users] segmentation fault in equilibrium

Dear Justin, Thank you from your response. No, there is not any warning from grompp. What is your idea? Best Regards Sara On Friday, November 13, 2015 1:02 AM, Justin Lemkul wrote: On 11/12/15 10:49 AM, mohammad agha wrote: > Dear Gromacs users, > > I have one system

Re: [gmx-users] segmentation fault in equilibrium

On 11/13/15 3:01 AM, sara soleimanzadegan wrote: Dear Justin, Thank you from your response. No, there is not any warning from grompp. What is your idea? Read the link I provided. Everything I would say is listed there. -Justin Best Regards Sara On Friday, November 13, 2015 1:02 AM,

Re: [gmx-users] segmentation fault in equilibrium

On 11/12/15 10:49 AM, mohammad agha wrote: Dear Gromacs users, I have one system consists 150 surfactants and 14000 solvent molecules and 200 water molecules by martini force field. When I want to reach my system to equlibrium with "mdrun pr", it isn't run and I have segmentation fault. Why

[gmx-users] segmentation fault in equilibrium

Dear Gromacs users, I have one system consists 150 surfactants and 14000 solvent molecules and 200 water molecules by martini force field. When I want to reach my system to equlibrium with "mdrun pr", it isn't run and I have segmentation fault. Why is it and what is the solution for this

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

On 10/24/15 4:41 PM, gozde ergin wrote: Also I tried the run these windows by using different computers and different Gromacs versions (5.0 and 5.1) however I always got the same segmentation fault error. Something about your physical model is unstable. Perhaps the topology, run settings,

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

Hi Justin, It is totally random. My system is 50 1-decanol2,4,8trimethyl molecules covered on 512 water molecules, Before, I did the umbrella sampling by using 1_decanol2468tetramethyl and 1-decanol as organic molecules and I did not get any error like this. Do you have any idea? Bests On Fri,

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

Also I tried the run these windows by using different computers and different Gromacs versions (5.0 and 5.1) however I always got the same segmentation fault error. On Sat, Oct 24, 2015 at 6:37 PM, gozde ergin wrote: > Hi Justin, > > It is totally random. My system is 50

[gmx-users] Segmentation fault in some windows of umbrella sampling

Dear users, I am doing umbrella sampling and using gromacs 4.6. I followed the Justin tutorial and generated 200 configurations on reaction coordinate. I faced segmentation fault error for 34 configurations (windows) but 166 of them run without any error. I thought maybe systems were not

Re: [gmx-users] Segmentation fault in some windows of umbrella sampling

On 10/23/15 11:38 AM, gozde ergin wrote: Dear users, I am doing umbrella sampling and using gromacs 4.6. I followed the Justin tutorial and generated 200 configurations on reaction coordinate. I faced segmentation fault error for 34 configurations (windows) but 166 of them run without any

[gmx-users] segmentation fault

Dear all, for applying electric field in gromacs-4.5.5 I should enter 3 numbers. The first one is number of cosines that should be 1. any number smaller than 1 is acceptable but when I use 1, grompp is done but mdrun doesnt start with the following error: segmentation fault. What should I do? Is

Re: [gmx-users] segmentation fault

On 7/19/15 8:32 PM, Sikandar Mashayak wrote: Hi, I am trying to simulate a confined water system with gromacs 5.0.5, however, I am getting the segmentation fault. Below are the gdb backtrace and the build info. Without an .mdp file and description of what you've done so far, there's little

[gmx-users] segmentation fault

Dear all, what is the solution for the segmentation fault after applying electric field? when I enter 1 for number of cosines mdrun doesnt start with segmentation fault error. does it mean that i can write any numbers as number of cosines and have stationary electric field or should i enter 1

[gmx-users] segmentation fault

Hi, I am trying to simulate a confined water system with gromacs 5.0.5, however, I am getting the segmentation fault. Below are the gdb backtrace and the build info. Thanks, Sikandar backtrace:: #0 0x7767d8dd in _mm_loadu_pd (tab_coul_F=0x7fffe6217100, tab_coul_V=0x7fffe621b560,

Re: [gmx-users] Segmentation fault (core dumped) version 4.6.*

of Carlos Navarro Retamal cnava...@utalca.cl Sent: 21 May 2015 11:55 To: gmx-us...@gromacs.org Subject: [gmx-users] Segmentation fault (core dumped) version 4.6.* Dear gmx users, In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed

[gmx-users] Segmentation fault (core dumped) version 4.6.*

Dear gmx users, In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella sampling simulations (and since the option pull_geometry=position is not available for the latest versions) For that, i installed the 4.6.7

Re: [gmx-users] Segmentation fault (core dumped) version 4.6.*

Retamal cnava...@utalca.cl Sent: 21 May 2015 11:55 To: gmx-us...@gromacs.org Subject: [gmx-users] Segmentation fault (core dumped) version 4.6.* Dear gmx users, In order to run my simulations, i usually used the 5.0.* version of gromacs without problems, but since i want to performed umbrella

[gmx-users] Segmentation fault (core dumped) during EM

Dear all, I want to simulate lid opening of lipase in presence of triglyceride micelle. I made micelle and equilibrate it in GROMACS (em, nvt, npt and md ) using CHARM36 force field. Dock triglyceride with lipase and put the docked complex close to micelle. I changed the atomtype after docking to

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

On 4/23/15 7:11 AM, Tushar Ranjan Moharana wrote: Dear all, I want to simulate lid opening of lipase in presence of triglyceride micelle. I made micelle and equilibrate it in GROMACS (em, nvt, npt and md ) using CHARM36 force field. Dock triglyceride with lipase and put the docked complex

Re: [gmx-users] Segmentation fault

Hi, I would not expect a good result from using both wrapper compilers and a collection of manually-specified include and library paths, because you have good chances of getting some detail wrong. Getting those right is a matter of following the docs for the MVAPICH2 + icc combination. In

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