[gmx-users] segmentation fault with mdrun

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 names from azide.top will be used atom names

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

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

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 the awkward

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

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

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

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

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

[gmx-users] segmentation fault after mdrun

Hello sir, Thanks for your suggestion.Then as u suggested i start the work from scratch and did the equilibriation again, there is nothing wrong with the topology also because it was taken from tiemann's website.The only message that it gives after equlibriation run is Steepest Descents

Re: [gmx-users] segmentation fault after mdrun

Nikit sharan wrote: Hello sir, Thanks for your suggestion.Then as u suggested i start the work from scratch and did the equilibriation again, there is nothing wrong with the topology also because it was taken from tiemann's website.The only message that it gives after equlibriation run is

Re: [gmx-users] segmentation fault after mdrun

Mark Abraham wrote: coulombtype = Cut-off In addition to everything Mark said, you should also *never* run a bilayer simulation with a simply cutoff scheme. You will get terrible artefacts. That goes for most other simulations too, but it has been demonstrated very recently

RE : RE : [gmx-users] segmentation fault in mdrun when using PME

Arneh Babakhani Date: mar. 2006-05-02 23:21 À: Discussion list for GROMACS users Objet : Re: RE : [gmx-users] segmentation fault in mdrun when using PME Hello, I'm experiencing the exact same problem, when trying to do some restrained molecular dynamics of a small peptide in a water box. Have you

RE: [gmx-users] segmentation fault in mdrun when using PME

-Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run

Re: [gmx-users] segmentation fault in mdrun when using PME

Diane Fournier wrote: -Original Message- From: [EMAIL PROTECTED] on behalf of David van der Spoel Sent: Sat 4/29/2006 2:25 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] segmentation fault in mdrun when using PME Diane Fournier wrote: Hi, I'm new to Gromacs

Re: [gmx-users] segmentation fault in mdrun when using PME

Diane Fournier wrote: Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan's Drug-Enzyme tutorial and mdrun crashes with segmentation fault and core dump at the steepest descents minimization step. However, mdrun

[gmx-users] segmentation fault in mdrun when using PME

Hi, I'm new to Gromacs and I'm trying to run a enzyme-ligand complex molecular dynamics simulation. I have tried doing John Kerrigan'sDrug-Enzyme tutorial and mdrun crashes withsegmentation fault and core dump at the steepest descents minimization step. However, mdrun works fine when using