Re: [gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Justin Lemkul
On 12/31/12 5:50 PM, Xu Dong Huang wrote: Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1star O12 0.430 0.000 0.000 1s

Re: [gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Xu Dong Huang
Ok I sent it. Let me know if you did not receive them. Xu Dong Huang Chemical & Biochemical Engineering Rutgers School of Engineering xudo...@eden.rutgers.edu On Dec 31, 2012, at 5:54 PM, Justin Lemkul wrote: > > > On 12/31/12 5:50 PM, Xu Dong Huang wrote: >> Dear Justin, >> >> I'm prett

Re: [gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Justin Lemkul
On 12/31/12 5:50 PM, Xu Dong Huang wrote: Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1star O12 0.430 0.000 0.000 1s

Re: [gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Xu Dong Huang
Dear Justin, I'm pretty sure my .gro file is valid, here is a direct copy and paste of the format of my .gro in the beginning: star polymer 201 1starO41 0.000 0.000 0.000 1starO12 0.430 0.000 0.000 1starO13 0.860 0.000 0.000

Re: [gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Justin Lemkul
On 12/31/12 5:40 PM, Xu Dong Huang wrote: Dear Justin, (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y) http://i1284.photobucket.com/albums/a571/X_huang1/Scr

Re: [gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Xu Dong Huang
Dear Justin, (here is the picture of the molecule after editconf, note the negative x and negative y axis is missing the rest of the beads that is suppose to be like the positive x and positive y) http://i1284.photobucket.com/albums/a571/X_huang1/ScreenShot2012-12-31at53618PM_zpse5f421f1.png *

Re: [gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Justin Lemkul
On 12/31/12 4:53 PM, Xu Dong Huang wrote: Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). Howev

[gmx-users] editconf not centering, and it is cutting off my molecule

2012-12-31 Thread Xu Dong Huang
Dear advanced gromacs users, I have created an arbitrary molecule .gro file containing coordinates of my martini-beads. basically, there are 50 beads sitting on each axis of (x,y, -x and -y) forming like a cross. (Each bead with distance 0.43). However, when I try to use editconf on my .gro fil