Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-13 Thread Shilpi Chaurasia
Dear Justin, Thanks a lot for your reply. Here I am providing the data and explaining the problem in detail: I hope that it will help you in understanding in a better way. Considering the tetramer as 'abcd'.  'ab' as one dimer and 'cd' as another, I want to separate 'ab' and 'cd'. Length

Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-13 Thread Justin A. Lemkul
Shilpi Chaurasia wrote: Dear Justin, Thanks a lot for your reply. Here I am providing the data and explaining the problem in detail: I hope that it will help you in understanding in a better way. Considering the tetramer as 'abcd'. 'ab' as one dimer and 'cd' as another, I want to separate

[gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-09 Thread Shilpi Chaurasia
 I am trying to pull apart two dimers of tubulin protein joined together, to form two separate dimers by steered molecular dynamics using Pull code. The objective is to separate the dimers by pulling along one axis only (Y axis). I ran the simulation for 25 ps and it accomplished well but while

Re: [gmx-users] pull code: distance between pull grp and ref grp is more than usual at the begining of simulation (at 1st time frame 1 ps)

2011-09-09 Thread Justin A. Lemkul
Shilpi Chaurasia wrote: I am trying to pull apart two dimers of tubulin protein joined together, to form two separate dimers by steered molecular dynamics using Pull code. The objective is to separate the dimers by pulling along one axis only (Y axis). I ran the simulation for 25 ps and it