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, 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

fault, core dumped error Hello gromacs users, I got an error message when I used gmx hbond command: Segmentation fault, core dumped. Shown below is my gmx version details (if that can point to my problem). Any insight would be appreciated. GROMACS version:2018.4 Precision: single