[gmx-users] Reg. thread MPI errror with gromacs-2016.4

Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on GPU.I run the production simulation using job file and it terminated with the fatal error: setting the number of thread-MPI ranks is only supported with thread-MPI and Gromacs was compiled without thread-MPI. Please gui

[gmx-users] Reg. thread MPI errror with gromacs-2016.4

Hello experts,I ran a MD simulation on HPC where Gromacs-2016.4 installed on GPU.I run the production simulation using job file and it terminated with the fatal error: setting the number of thread-MPI ranks is only supported with thread-MPI and Gromacs was compiled without thread-MPI. Please gui

[gmx-users] Reg. mdrun error: not all ion group molecules consist of 3 atoms

Hello,I am performing computational Electrophysiology gromacs tutorial.  I successfully pass the grompp for the compEL but failed with a Fatal error at mdrun step, not all ion group molecules consist of 3 atoms.my command for grompp was gmx_mpi_d grompp -f step7-prod.mdp -o step7-prod.tpr -c st

[gmx-users] Reg. mdrun error: not all ion group molecules consist of 3 atoms

Hello,I am performing computational Electrophysiology gromacs tutorial.  I successfully pass the grompp for the compEL but failed with a Fatal error at mdrun step, not all ion group molecules consist of 3 atoms.my command for grompp was gmx_mpi_d grompp -f step7-prod.mdp -o step7-prod.tpr -c st

Re: [gmx-users] Error while running perl distances.pl

uot;Vytautas Rakeviius " To: gmx-us...@gromacs.org,gromacs.org_gmx-users@maillist.sys.kth.se,가디 장데부 고라크스나트 Cc.: gadhe.chang...@gmail.com Sent date: 2017-09-04 15:36:29 GMT +0900 (Asia/Seoul) Title: Re: [gmx-users] Error while running perl distances.pl Script assumes that variable

[gmx-users] Error while running perl distances.pl

Hello Gmx user, I would like to transport solute molecule from the ion channel (intracellular to extracellular site) using steered MD and umbrella sampling method to calculate the energy. I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but in distance.pl it shows s

[gmx-users] Error while running perl distances.pl

Hello Gmx user, I would like to transport solute molecule from the ion channel (intracellular to extracellular site) using steered MD and umbrella sampling method to calculate the energy. I followed Dr. Lemkul's tutorial and it works fine upto equilibration step but in distance.pl it shows s

[gmx-users] InflateGRO script

Hello there, This is Changdev and I am facing problem in InflateGRO script. I am working on membrane protein and would like to embed the protein into 512 DPPC lipids. I used the command from Dr. Justin's tutorial. perl inflategro.pl system.gro 4 DPPC 14 sys_infl.gro 5 area.dat after running t

[gmx-users] Reg. Umbrella sampling problem with direction

Hello Everyone, I am novice in umbrella sampling. I did followed Dr. Justin's tutorial and it works fine for me. However, I would like to transport solute (along z-axis) from an ion channel (intracellular to extracellular site) so I made the system (Protein+solute+DPPC+Sol+ion) and came upto t

[gmx-users] Reg. Umbrella sampling problem with direction

Hello Everyone, I am novice in umbrella sampling. I did followed Dr. Justin's tutorial and it works fine for me. However, I would like to transport solute (along z-axis) from an ion channel (intracellular to extracellular site) so I made the system (Protein+solute+DPPC+Sol+ion) and came upto t