Re: [gmx-users] Centering the system

2013-10-17 Thread Shima Arasteh
I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee? Thanks a lot. Sincerely, Shima On Wednesday, October 16, 2013 4:05 PM, Justin Lemkul jalem...@vt.edu wrote: On 10/16/13 8:29 AM, Shima

Re: [gmx-users] Centering the system

2013-10-17 Thread Justin Lemkul
On 10/17/13 2:09 PM, Shima Arasteh wrote: I used -fit or boxcenter or trans or .. any other thing which I though to solve my problem, but did not work. Would you give me a hint pleaaasssee? trjconv -center or trjconv -fit transxy -Justin --

[gmx-users] Centering the system

2013-10-16 Thread Shima Arasteh
Dear gmx users, I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups. It's ok, but the peptide is near one edge of

Re: [gmx-users] Centering the system

2013-10-16 Thread Justin Lemkul
On 10/16/13 8:29 AM, Shima Arasteh wrote: Dear gmx users, I have a system consist of a lipid bilayer and a peptide. As the initial configuration, the peptide is located in center of the x-y plane above lipid bilayer. After running MD, the peptide shows interactions with the polar groups.

Re: [gmx-users] Centering the system

2013-10-16 Thread Андрей Гончар
Hi. You should use the following command to center your protein: trjconv -f trajectory.xtc -o corrected_trajectory.xtc -pbc mol -center -s trajectory.tpr Don't forget to replace trajectory with corresponding filenames 2013/10/16 Shima Arasteh shima_arasteh2...@yahoo.com Dear gmx users, I