Re: [gmx-users] Transition difficulties: version 3.3.3 to 4.0.3 regarding pull_geometry=distance

Hi, I rebuilt the code using both sets of Berk's corrections. On an isolated bilayer system with no periodic boundaries in the x-y plane prepared in the manner previously explained, the recompiled grompp output yielded no improvement in the discrepancies of the position of a buckyball permea

Re: [gmx-users] freez group

Morteza Khabiri wrote: Dear Users, I have a ligand inside one protein which I should freeze them to equilibrate the solution around the protein. Unfortunately after some ps the structure of protein and the environmental solution start to crash to each other. Before I start mdrun, after grompp I

[gmx-users] freez group

Dear Users, I have a ligand inside one protein which I should freeze them to equilibrate the solution around the protein. Unfortunately after some ps the structure of protein and the environmental solution start to crash to each other. Before I start mdrun, after grompp I get the following error:

[gmx-users] restore pbc after a rotation

Dears, I need to rerun a trajectory that has been rotated to orient a molecule according to a reference. The pbc are therefore broken. Would anyone know how to restore the correct position of the atoms inside the unit cell after the rotation is applied. The rotation is actually applied arou