Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

2018-01-12 Thread Justin Lemkul
On 1/12/18 7:09 AM, rose rahmani wrote: I had this problem but i couldn't solve it. But i can tell you just a temporary solution; Don't use -sep with trjconv,then use the output conf as an input for gmx distance. it probably gives you sth like this; time distances

Re: [gmx-users] umbrella sampling Protein_ligand complex distance calculation

2018-01-12 Thread rose rahmani
I had this problem but i couldn't solve it. But i can tell you just a temporary solution; Don't use -sep with trjconv,then use the output conf as an input for gmx distance. it probably gives you sth like this; time distances 0.0001.75372870.02386010.0428935

[gmx-users] umbrella sampling Protein_ligand complex distance calculation

2018-01-11 Thread Ashwini Londhe
Hi Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very fine. so I following the same tutorial for ligand-protein complex. I have pulled the ligand over 300ps using following MD_pull.mdp and also generated series of cordinate files (conf0.gro-conf300.gro) but problem is