[gmx-users] pbc-replica exchange-trjconv

For a given temperature, I will make them continues again then before analysis. Thanks for the help! kind regards, servaas Hoi Servaas, Was that the trajectory for a given temperature, or for a given system? It should be for the latter, as otherwise, there will be weird shifts introduced.

Re: [gmx-users] pbc-replica exchange-trjconv

Hi Servaas, > trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr I think there's quite a bit of reason to start calling you names here :) Assumedly, fit.trr means that it results from fitting the trajectory to a reference? So what does this do with your PBC? > I also tr

Re: [gmx-users] pbc-replica exchange-trjconv

servaas michielssens wrote: Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box. The trajectory is generated by replica exchange simulation. So I used trjconv with the option cluster: trjco

[gmx-users] pbc-replica exchange-trjconv

Dear gromacs users, I have a problem that is already discussed a lot on the mailing list, in a protein-ligand simulation the ligad jumps out of the box. The trajectory is generated by replica exchange simulation. So I used trjconv with the option cluster: trjconv -f fit.trr -o cluster.trr -n