[gmx-users] Question on generating hydrogens

Hi all, Is it possible to use pdb2gmx to generate hydrogens for a configuration file without also creating a topology file? Based on the documentation, it seems I can only rename this file, not prevent its creation. Ideally, I'd like to prevent this, because I have many

[gmx-users] (no subject)

* * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received

[gmx-users] Replica exchange question?

Hello all;i want to perform a REMD simulation with orientation restraint added, and i want to make sure that my scheme is correct so i have a few questions:1)  if i have dihedral restraint or/and orientation restraint they should be added in all steps ( energy minimization, temperature

[gmx-users] how can I obtain the potential energy of each atom？

Hi, I want to extract the potential energy of each atom. Unfortunately, gmx_energy don't provide the potential energy of each.So,how can I obtain the potential energy of each atom ? Thanks!Best regards,Ke

[gmx-users] Failed tests, need help in troubleshooting

Hello, I have installed gromacs 2019.1 on CentOS 7.6 . While running regressions tests 2019.1 certain tests are failing with errors. I have attached list of some failed tests. Since I am using gcc compilers and openmpi from openhpc repositories the below command was used for cmake.