Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Justin, Thanks for the options suggested. I have used -princ and rotate 0 0 90 options with editconf and was able to place the protein vertically and at the centre of the DPPC bilayer (128 + 3655) from the site provided in the tutorial, but still the part of protein is out

Re: [gmx-users] step 0Segmentation fault

Dear Justin, Thanks for the options suggested. I have used -princ and rotate 0 0 90 options with editconf and was able to place the protein vertically and at the centre of the DPPC bilayer (128 + 3655) from the site provided in the tutorial, but still the part of protein is outside the DPPC layer

Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Justin, As suggested, when i reexamined the system.gro (protein_newbox + dppc128) one of the ends of the problem (as i think) i.e. few aminoacids of protein were beyond the water surface of the bilayer, probably this may be the reason for the presence of water molecules to

Re: [gmx-users] step 0Segmentation fault

Dear Justin, As suggested, when i reexamined the system.gro (protein_newbox + dppc128) one of the ends of the problem (as i think) i.e. few aminoacids of protein were beyond the water surface of the bilayer, probably this may be the reason for the presence of water molecules to the side of the bil

Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Justin, Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. Peter Tieleman website, and the nvt.mdp file and the nvt.log files are as follows as in your tutorial: Constraining the starting coordinates (step 0) Constraining the coordinates at t0-dt (st

Re: [gmx-users] step 0Segmentation fault

Dear Justin, Thanks for the advice. I am using the DPPC 128 lipid bilayer from D. Peter Tieleman website, and the nvt.mdp file and the nvt.log files are as follows as in your tutorial: _

Re: [gmx-users] step 0Segmentation fault

ram bio wrote: Dear Gromacs Users, I have inserted the protein in lipid bilayer and performed Inflategro I am able to reach the required area per lipid after certain iterations but was unable to get the standard Epot and Fmax values that is negative and to the power of 5 or 6 and Fmax less tha