[gmx-users] Biphasic Systems

Dear Gmx Users, I made a biphasic system with water and hexane following Justin tutorial  (800 hexane molecules) ,after adding the peptides in water phase, the number of the hexane molecules were reduced and some of them were shifted to the other side of water molecules (not at the interface of

[gmx-users] NVT input file

Dear Gromacs users, Does anyone know how to change the NVT input file for Justin tutorial (lysozymein a box of water), so that the temperature is slowly increased from 50K to 300K?, any general advise or modification of input file is highly appreciated. Cheers Davoud -- gmx-users mailing list

[gmx-users] NVT input file

Dear Gromacs users, Does anyone know how to change the NVT input file for Justin tutorial (lysozymein a box of water), so that the temperature is slowly increased from 50K to 300K? the nvt of the tutorial is attached, any general advise or modification of input file is highly appreciated. Cheers

[gmx-users] Question

Dear Sir I am a newbie on Gromacs. I am trying to solvate my protein (1CJ5.pdb) with water. I am following the tutorial by Justin Lemkul but when I execute the following command pdb2gmx -f 1CJ5.pdb -o 1CJ5_processed.gro -water spce and choose OPLS-AA/L all-atom force field I am getting an fatal