[gmx-users] error during mdrun

Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error like this Fatal error: 6 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of

Re: [gmx-users] error during mdrun

On 11/29/12 7:49 AM, Shine A wrote: Sir, I am studying the dynamics of membrane proteins using KALP-15 in DPPC. Now doing nvt equilibration.During mdrun (mdrun -deffnm nvt) getting error like this Fatal error: 6 particles communicated to PME node 1 are more than 2/3 times the cut-off

[gmx-users] error in mdrun

Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein. Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02, atom= 1653 Stepsize too small, or no change in energy. Converged to machine

[gmx-users] error in mdrun (2)

When I run the md run again I get still the already mentioned error and additionally this one: Fatal error: 66 particles communicated to PME node 2 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

Re: [gmx-users] error in mdrun

On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi everybody, I want to do a md for a protein with a membrane around it. I already minimised the energy of the protein. Output of the minimization: ^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02,

Re: [gmx-users] error in mdrun

Hi Justin, okey then I will try it with this timestep. No it is not my goal to do a NVE. I already had temperature coupling options in my .mdp file but on the blowing up side was written you are using inappropriate temperature coupling so I thought that that might be the reason and deleted it

Re: [gmx-users] error in mdrun

On 7/9/12 9:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: Hi Justin, okey then I will try it with this timestep. No it is not my goal to do a NVE. I already had temperature coupling options in my .mdp file but on the blowing up side was written you are using inappropriate

Re: [gmx-users] error in mdrun

With the mentioned below options I get the following error: Fatal error: 1 particles communicated to PME node 1 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. But it

Re: [gmx-users] error in mdrun

On 7/9/12 9:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: With the mentioned below options I get the following error: Fatal error: 1 particles communicated to PME node 1 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension x.

Re: [gmx-users] error in mdrun

I already decrease it to 0.002 as you said and then there comes this error I wrote to you. Now It try it with 0.001. It is still running. Thank you for your answer. Eva On 7/9/12 9:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote: With the mentioned below options I get the following

[gmx-users] Error after Mdrun

Dear all, I need some help in my simulation. I Put system(dppc bilayer) in a cubic box then solvated it and made a equlibriation run.There were no issues till then.But when i proceded with the production run , the simulation crashes in no more than 5 or 10 steps leaving an error message

Re: [gmx-users] Error after Mdrun

Nikit sharan wrote: Dear all, I need some help in my simulation. I Put system(dppc bilayer) in a cubic box then solvated it and made a equlibriation run.There were no issues till then. Check again for warnings, and pay attention to them :-) But when i proceded with the production run ,

[gmx-users] Error of mdrun

Dear Experts, Hi ! I am doing MD simulation on two computer, on one when I want to start the EM and do the mdrun command the following error results: linux:~/project # mdrun -v -s em.tpr -c em.pdb mdadm: /dev/md-v not identified in config file. linux:~/project # mdrun -v -deffnm em mdadm:

Re: [gmx-users] Error of mdrun

s lal badshah wrote: Dear Experts, Hi ! I am doing MD simulation on two computer, on one when I want to start the EM and do the mdrun command the following error results: linux:~/project # mdrun -v -s em.tpr -c em.pdb mdadm: /dev/md-v not identified in config file. linux:~/project # mdrun -v

[gmx-users] Error of mdrun

Dear Mark, When I enter from root account the following is the result: linux:~ # which mdrun /sbin/mdrun linux:~ # which grompp /usr/bin/grompp linux:~ # But from user account the which mdrun usr/bin/mdrun and also the which grompp /usr/bin/grompp occured. Actually I have very little

[gmx-users] error in mdrun

Hi all, I installed the gromacs on my system. The pdb2gmx, editconf,grompp,.. are ok,but when I try to do mdrun I have this error: mdadm: /dev/md-v not identified in config file. Any ideas in this relation? Thanks

Re: [gmx-users] error in mdrun

Hi Mohammad, Seems this is your problem: http://www.penguin-soft.com/penguin/man/8/mdrun.html Not quite the mdrun you meant to be running. Make sure that the gromacs directory comes first in the path or link/copy it under a different name. Best, Tsjerk On 9/29/07, Mohammad Ahmadi [EMAIL

[gmx-users] Error during mdrun

Dear all, At times during the md run of my peptide, the run crashes and I get the following error displayed - Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates MPI process rank 0 (n0, p3089) caught a SIGSEGV. MPI process rank 1 (n0,

Re: [gmx-users] Error during mdrun

Dear all, At times during the md run of my peptide, the run crashes and I get the following error displayed - Wrote pdb files with previous and current coordinates Wrote pdb files with previous and current coordinates MPI process rank 0 (n0, p3089) caught a SIGSEGV. MPI process rank 1 (n0,

Re: [gmx-users] Error during mdrun

Hi Chetana (and Mark et al.), Note that this can also be the infamous spinning -NH3 error, which has been reported primarily for lysines previously on this list (tip: search the archive). To be sure, as Mark stated, more information is required. Specifically, at what step the crash occurred and

Re: [gmx-users] Error during mdrun

(Now why am I always lagging behind Mark with my comments?)... I'm writing up a thesis and have nothing else to do but sit online? :-) Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please

[gmx-users] Error during mdrun

Thanks, Tsjerk and Mark. Here's what the end of my log file says : Step Time Lambda 524390010487.800780.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.019872 61 62 0.004609 After

Re: [gmx-users] Error during mdrun

chetana baliga wrote: Thanks, Tsjerk and Mark. Here's what the end of my log file says : Step Time Lambda 524390010487.800780.0 Rel. Constraint Deviation: Maxbetween atoms RMS Before LINCS 0.019872 61 62

[gmx-users] error after mdrun

Dear All I am new to gromacs...please help me and let me know how to proceed..when i give the mdrun command he terminal displays the following: /usr/local/gromacs/bin/mdrun -nice 0 -v -s hyb2b_vac_md.tpr -o hyb2b_vac_md_1ns_traj.trr -c hyb2b_vac_md_1ns.gro -e hyb2b_vac_md_1ns_ener.edr -g

Re: [gmx-users] error after mdrun

nur avneet wrote: Dear All I am new to gromacs...please help me and let me know how to proceed..when i give the mdrun command he terminal displays the following: /usr/local/gromacs/bin/mdrun -nice 0 -v -s hyb2b_vac_md.tpr -o hyb2b_vac_md_1ns_traj.trr -c hyb2b_vac_md_1ns.gro -e

[gmx-users] error with mdrun

Hi , i am trying to do an mdrun and i get the following messageELAN_EXCEPTION @ --: 6 (Initialisation error) elan_init: Cant get capability from environmentAborted does anyone have any idea from where that error comes from ?___ gmx-users mailing list

Re: [gmx-users] error with mdrun

Argyrios Karatrantos wrote: Hi , i am trying to do an mdrun and i get the following message ELAN_EXCEPTION @ --: 6 (Initialisation error) elan_init: Can't get capability from environment Aborted from your mpi library. check that you've initialized your mpi system correctly. does anyone

Re: [gmx-users] error with mdrun

Argyrios Karatrantos wrote: Hi , i am trying to do an mdrun and i get the following message ELAN_EXCEPTION @ --: 6 (Initialisation error) elan_init: Can't get capability from environment Aborted does anyone have any idea from where that error comes from ? It's got something to do with

[gmx-users] Error with mdrun

Hi, I am trying to run a lipid bilayer simulation, and everything seems to be fine until I try to run mdrun. The simulation stops immediately after I begin mdrun, and I receive the error; p4_error: interrupt SIGSEV: 11. I am not really sure what this error is, nor what I should do to try

RE: [gmx-users] Error with mdrun

I am trying to run a lipid bilayer simulation, and everything seems to be fine until I try to run mdrun. The simulation stops immediately after I begin mdrun, and I receive the error; p4_error: interrupt SIGSEV: 11. I am not really sure what this error is, nor what I should do to

Re: [gmx-users] Error with mdrun

[EMAIL PROTECTED] wrote: Hi, I am trying to run a lipid bilayer simulation, and everything seems to be fine until I try to run mdrun. The simulation stops immediately after I begin mdrun, and I receive the error; p4_error: interrupt SIGSEV: 11. I am not really sure what this error is, nor