Re: [gmx-users] Distances calculation in umbrella sampling

2017-12-01 Thread Amir Zeb
Hi Replace the name of groups in original script by the names in between which you want to measure the distance Good luck! On Dec 1, 2017 5:50 PM, "Kingsley Theras Primus Dass ." < 105726...@gms.tcu.edu.tw> wrote: > dear users, > I am encountering a problem with script, the summary.dat file

Re: [gmx-users] Distances calculation in umbrella sampling

2017-12-01 Thread Kingsley Theras Primus Dass .
dear users, I am encountering a problem with script, the summary.dat file does not generate any value. But if I run the distance command one at the time , it is generating the value, I could not figure out where I am goingperlgmx wrong. can anyone tell where lies the mistake?mistake? Thank you

Re: [gmx-users] Distances calculation in umbrella sampling

2017-11-30 Thread Amir Zeb
Solved it, Thanks every one! Amir On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul wrote: > > > On 11/30/17 4:04 AM, Rose wrote: > >> Till nowi think the only solution is to use gmx distance for each >> conf.gro files.then use perl script. >> don't forget to delete gmx distance

Re: [gmx-users] Distances calculation in umbrella sampling

2017-11-30 Thread Justin Lemkul
On 11/30/17 4:04 AM, Rose wrote: Till nowi think the only solution is to use gmx distance for each conf.gro files.then use perl script. don't forget to delete gmx distance line from script. Or run one instance of gmx distance manually to understand how to properly use it, diagnose any

Re: [gmx-users] Distances calculation in umbrella sampling

2017-11-30 Thread Rose
Till nowi think the only solution is to use gmx distance for each conf.gro files.then use perl script. don't forget to delete gmx distance line from script. -Rose Sent from my iPhone > On Nov 30, 2017, at 10:28, Amir Zeb wrote: > > Hello gmx users, > > I want to

[gmx-users] Distances calculation in umbrella sampling

2017-11-29 Thread Amir Zeb
Hello gmx users, I want to calculate binding free energy for protein-ligand complex by Umbrella sampling in Gromacs. I have extracted each frame's gro file for 500 frames after pulling simulation. Now, I want to calculate the distances between the representative gro files by executing the script