Hi, Kush, I have a question. Hope you can help me. Here you load md_0_1.gro structure, but I usually use npt.gro structure instead. I thought that npt.gro is initial file for md production, and md_0_1.gro is final structure (coordinates of all atoms at last frame of trajectory). So, which one (npt.gro or md_0_1.gro) should I use in VMD as a molecule? Initial or final?
Why is it that I can view my trajectories only in certain representations while in lines/bonds representation I get these messy visualization as in the beginning of this video? Is line drawing style not compatible with gromacs trajectories?
Hi I have a protein ligand complex... I am getting error running gromacs in ionisation step stating "invalid order of directive atomtypes'...how can I fix this error.
Hi, Kush, I have a question. Hope you can help me. Here you load md_0_1.gro structure, but I usually use npt.gro structure instead. I thought that npt.gro is initial file for md production, and md_0_1.gro is final structure (coordinates of all atoms at last frame of trajectory). So, which one (npt.gro or md_0_1.gro) should I use in VMD as a molecule? Initial or final?
what is the difference between npt.gro and md_0_1.gro? for me, idk why but md_0_1.gro is not generated
why few of your atom are stretech with length equal to box??
what do you make of that blip at about 2:49?
therealrictuar sorry I didn’t get it
more like at 2:51
the protein seems to display a radically different shape for a single frame. What do you make of that?
Why is it that I can view my trajectories only in certain representations while in lines/bonds representation I get these messy visualization as in the beginning of this video? Is line drawing style not compatible with gromacs trajectories?
And how to remove the PBC condictions, the jumps of solvent...?
DR. Kush Kindly suggest link for Molecular dynamic simulation Protocol/methods by gromacs or by VMD
Mohammad hayatul islam sir if you have any quey pls mail me on kushmehta2325@gmail.com
thankyou, its really helpful😊😊
How should I select only the ligand?
Thank you! really helpful!
Hi I have a protein ligand complex... I am getting error running gromacs in ionisation step stating "invalid order of directive atomtypes'...how can I fix this error.
i think u r using charm ff for which u have to set bond order during ligand topology file generation
Thanks!