[gmx-users] Order parameter calculation

Hi all, I am trying to calculate order parameter for DPPC monolayer using do-order-milti.py script.Actually, the monolayer consists of 716 CG DPPC and 307 CG POPG lipid molecules. The system consists two such monolayer separated by a water slab. I run the simulation for 3 microsecond and renamed

[gmx-users] membrane simulation

Hi Dear all I have a protein with three parts: inter-membrane, transmembrane, outer-membrane regions I want to simulate this protein into a membrane, please let me know how to set this protein into the membrane which for example the amino acids located in outer-membrane and the exact amino acids

[gmx-users] Umbrella Sampling with Direction-Periodic Pulling

Hello, I am using a pull code with geometry=direction-periodic and attempting to use gmx wham to construct the free energy. I believe the pulling code is doing what I would like it to, but as might be expected from direction-periodic, when the pull distance is more than half the box length the

[gmx-users] ATB and PRODRG

Dear gmx users I am using gromos96 54 a7 and gromos 96 a1 force fiels to simulate tow various complexes  ( protein + ligand). and  used ATB and PRODRG  to create topology files for them, respectively. I dont know anything about editing ATB and PRODRG' topology files but reassigingn their

Re: [gmx-users] Did -ndec stop working in 2016 releases?

Thanks, I will have a look, since unfortunately my code currently relies on ASCII trajectories to work, and removing the extra precision I need would not work for me. I think it could help to print a warning when the user requests .gro files and non-stardard precision. Miguel -- Dr.