[gmx-users] Recreating newer TPRs for old Gromacs

Dear all, For the purpose of a project I am trying to recreate TPRs so I can use them with an older version of Gromacs. The TPR files in question are: - ion channel: https://repository.prace-ri.eu/ueabs/GROMACS/1.2/GROMACS_TestCaseA.tar.gz - lignocellulose:

[gmx-users] First beta release of GROMACS 2020

Hi GROMACS users, The first beta release of GROMACS 2020 is available! We are making this available to you to get an early taste of how GROMACS 2020 will look and work, and most importantly to get feedback from you about how well things work. While we try our hardest to keep the quality of

Re: [gmx-users] Ligand molecule occupancy

On 9/25/19 5:46 AM, Pandya, Akash wrote: Hi, I have multiple ligand molecules of the same type in my system. If I wanted to monitor the Cartesian coordinates of each individual ligand during a simulation, is there a Gromacs tool to do that? or do I have write a custom script? You can

Re: [gmx-users] Umbrella sampling on lipid bilayer

On 9/25/19 5:50 AM, Mahsa Rezaei wrote: Dear Dr. Warren Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD ,

Re: [gmx-users] Umbrella sampling on lipid bilayer

Dear Dr. Warren Unfortunately,I missed your reply! Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD ,

[gmx-users] Umbrella sampling on lipid bilayer

Dear Dr. Warren Thanks for your response . I made my protein-membrane system with charmm-gui. so my force is charmm36. I used the equilibration input files that charmm-gui provide , and run 400 ns simulation for equilibration of my system . RMSD , temperature and pressure is good , so I

[gmx-users] Ligand molecule occupancy

Hi, I have multiple ligand molecules of the same type in my system. If I wanted to monitor the Cartesian coordinates of each individual ligand during a simulation, is there a Gromacs tool to do that? or do I have write a custom script? Some background: My purpose is to look at

Re: [gmx-users] issues running virus capsid simulation

Den 2019-09-25 kl. 02:37, skrev Justin Lemkul: On 9/24/19 5:09 PM, Asis Jana wrote: Hi, I am doing viral capsid simulation using GROMACS 2018. The capsid was first energy minimized using the steepest-descent algorithm followed by 40 ns of NVT (300 K) followed by 10 ns of NPT (300 K, 1