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. Then when > > we moved to a larger and more complicated system we started getting > > mdrun segmentation faults during "steep" energy minimization. This > > happens on our cluster and on our iMacs. > > > > > > > > Any help would be appreciated. Also I can attach my mdp files. > > > > > > There are a whole host of things that could be going wrong. Without > substantially more information, including even more (like a thorough description > of what these systems are and the exact commands of what worked before), then > you won't get any useful advice. > > -Justin > Ok, system 1 that worked is biotin and strepavidin in a water box, and the "larger" system is just rifampicin in a water box for hydration energies. Both ligands are being removed via FEP. As for commands they are identical as we have made a systematic script that sets up our systems. It is: pdb2gmx -f base.pdb -o base.gro -p base.top ===Here we put the ligand .gro and the protein "base" .gro together. editconf -bt cubic -f base.gro -o base.gro -c -d 3.5 genbox -cp base.gro -cs spc216.gro -o base_b4ion.gro -p base.top grompp -f em.mdp -c base_b4ion.gro -p base.top -o base_b4ion.tpr -maxwarn 2 genion -s base_b4ion.tpr -o base_b4em.gro -neutral -conc 0.01 -pname NA -nname CL -g base_ion.log -p base.top ==Here select SOL grompp -f em.mdp -c base_b4em.gro -p base.top -o base_em.tpr mdrun -v -s base_em.tpr -c base_after_em.gro -g emlog.log -cpo stat_em.cpt ===Segmentation fault occurs here. grompp -f pr.mdp -c base_after_em.gro -p base.top -o base_pr.tpr mdrun -v -s base_pr.tpr -e pr.edr -c base_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt -dhdl dhdl-pr.xvg grompp -f md.mdp -c base_after_pr.gro -p base.top -o base_md.tpr mdrun -v -s base_md.tpr -o base_md.trr -c base_after_md.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dhdl dhdl-md.xvg grompp -f FEP.mdp -c base_after_md.gro -p base.top -o base_fep.tpr mdrun -v -s base_fep.tpr -o base_fep.trr -c base_after_fep.gro -g fep.log -e fep.edr -cpi state_fep.cpt -cpo state_fep.cpt -dhdl dhdl-fep.xvg I can include mdp files if that would help. Yes, please do. -Justin Thank you, TJ Mustard > > > > Thank you > > > > > > > > TJ Mustard > > Email: musta...@onid.orst.edu > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > TJ Mustard Email: musta...@onid.orst.edu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 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 minimization. This > > happens on our cluster and on our iMacs. > > > > > > > > Any help would be appreciated. Also I can attach my mdp files. > > > > > > There are a whole host of things that could be going wrong. Without > substantially more information, including even more (like a thorough description > of what these systems are and the exact commands of what worked before), then > you won't get any useful advice. > > -Justin > Ok, system 1 that worked is biotin and strepavidin in a water box, and the "larger" system is just rifampicin in a water box for hydration energies. Both ligands are being removed via FEP. As for commands they are identical as we have made a systematic script that sets up our systems. It is: pdb2gmx -f base.pdb -o base.gro -p base.top ===Here we put the ligand .gro and the protein "base" .gro together. editconf -bt cubic -f base.gro -o base.gro -c -d 3.5 genbox -cp base.gro -cs spc216.gro -o base_b4ion.gro -p base.top grompp -f em.mdp -c base_b4ion.gro -p base.top -o base_b4ion.tpr -maxwarn 2 genion -s base_b4ion.tpr -o base_b4em.gro -neutral -conc 0.01 -pname NA -nname CL -g base_ion.log -p base.top ==Here select SOL grompp -f em.mdp -c base_b4em.gro -p base.top -o base_em.tpr mdrun -v -s base_em.tpr -c base_after_em.gro -g emlog.log -cpo stat_em.cpt ===Segmentation fault occurs here. grompp -f pr.mdp -c base_after_em.gro -p base.top -o base_pr.tpr mdrun -v -s base_pr.tpr -e pr.edr -c base_after_pr.gro -g prlog.log -cpi state_pr.cpt -cpo state_pr.cpt -dhdl dhdl-pr.xvg grompp -f md.mdp -c base_after_pr.gro -p base.top -o base_md.tpr mdrun -v -s base_md.tpr -o base_md.trr -c base_after_md.gro -g md.log -e md.edr -cpi state_md.cpt -cpo state_md.cpt -dhdl dhdl-md.xvg grompp -f FEP.mdp -c base_after_md.gro -p base.top -o base_fep.tpr mdrun -v -s base_fep.tpr -o base_fep.trr -c base_after_fep.gro -g fep.log -e fep.edr -cpi state_fep.cpt -cpo state_fep.cpt -dhdl dhdl-fep.xvg I can include mdp files if that would help. Thank you, TJ Mustard > > > > Thank you > > > > > > > > TJ Mustard > > Email: musta...@onid.orst.edu > > > > -- > > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
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 minimization. This happens on our cluster and on our iMacs. Any help would be appreciated. Also I can attach my mdp files. There are a whole host of things that could be going wrong. Without substantially more information, including even more (like a thorough description of what these systems are and the exact commands of what worked before), then you won't get any useful advice. -Justin Thank you TJ Mustard Email: musta...@onid.orst.edu -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
[gmx-users] Segmentation Fault in EM
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 minimization. This happens on our cluster and on our iMacs. Any help would be appreciated. Also I can attach my mdp files. Thank you TJ Mustard Email: musta...@onid.orst.edu -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
