Re: [gmx-users] concatenate tpr files for PCA analysis

Dear Subhomoi and Mark, I was able to overcome the problem by using the new tpr file, as suggested. Thanks for the help. Regards. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

Re: [gmx-users] How to calculate the force between two specified groups in Gromacs

Hi, I used this tool for my protein, not sure if it would work for you: https://github.com/HITS-MBM/gromacs-fda/releases https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-101 It calculates pair-wise forces between individual residues and you can choose between scalar or

Re: [gmx-users] No constraints, default potential?

Hi, Whatever is in your topology (unless you used the mdp option that converts harmonic to Morse). Generally that is harmonic. Mark On Sun., 21 Apr. 2019, 01:13 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > When no bond constraints are applied

Re: [gmx-users] Cannot select termini with AMBER99sb-ildn

Hi, IIRC they chose not to parametrize for things that would not be present in the systems they intended to model. Mark On Sun., 21 Apr. 2019, 01:21 Neena Susan Eappen, < neena.susaneap...@mail.utoronto.ca> wrote: > Hello gromacs users, > > I was wondering why with AMBER99sb-ildn force field,

Re: [gmx-users] Help for GROMACS best performance system

Hi, The recent paper https://arxiv.org/abs/1903.05918 is excellent for these questions, and more! Mark On Sat., 20 Apr. 2019, 21:09 Ali Sufali, wrote: > Hi > > It's been a while I have started using GROMACS for my researches and now I > want to buy a system with powerful performance. > > I