[gmx-users] Center of mass: distance restrain for groups

2011-10-10 Thread Li, Hualin
Dear GMX users, I am using pull code to make a distance restrain to my proteins and membrane,which looks like this: pull = umbrella pull_geometry= cylinder pull_vec1 = 0 0 1 pull_r1 = 2.5 pull_r0 = 2.5 pull_dim =

RE: [gmx-users] Center of mass: distance restrain for groups

2011-10-10 Thread Li, Hualin
Dear GMX users, I am using pull code to make a distance restrain to my proteins and membrane,which looks like this: pull = umbrella pull_geometry= cylinder pull_vec1 = 0 0 1 pull_r1 = 2.5 pull_r0 = 2.5 pull_dim =

RE: [gmx-users] Center of mass: distance restrain for groups

2011-09-27 Thread Li, Hualin
gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf > Of Justin A. Lemkul [jalem...@vt.edu] > Sent: Monday, September 26, 2011 1:32 PM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Center of mass: distance restrain for groups > > Justin A

Re: [gmx-users] Center of mass: distance restrain for groups

2011-09-27 Thread Justin A. Lemkul
it this keyword. -Justin Best, Hualin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 1:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of ma

RE: [gmx-users] Center of mass: distance restrain for groups

2011-09-27 Thread Li, Hualin
[gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 1:32 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distance restrain for groups Justin A. Lemkul wrote: > > > Li, Hualin wrote: >> I a

Re: [gmx-users] Center of mass: distance restrain for groups

2011-09-26 Thread Justin A. Lemkul
Justin A. Lemkul wrote: Li, Hualin wrote: I am sorry about the last post, I mean "I am not sure about the word "pullumbrella", is this command used in free energy calculation to do the sampling ? I am not doing the free energy calculation, should I change something in the

Re: [gmx-users] Center of mass: distance restrain for groups

2011-09-26 Thread Justin A. Lemkul
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 12:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distance restrain for groups Li, Hualin wrote: Dear G

RE: [gmx-users] Center of mass: distance restrain for groups

2011-09-26 Thread Li, Hualin
Thanks, Hualin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 12:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distan

RE: [gmx-users] Center of mass: distance restrain for groups

2011-09-26 Thread Li, Hualin
ase? Thanks, Hualin From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: Monday, September 26, 2011 12:05 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Center of mass: distance restrain for groups Li, Hual

Re: [gmx-users] Center of mass: distance restrain for groups

2011-09-26 Thread Justin A. Lemkul
Li, Hualin wrote: Dear GMX users, How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of speci

[gmx-users] Center of mass: distance restrain for groups

2011-09-26 Thread Li, Hualin
Dear GMX users, How are you doing? I have a question about using distance restrain in GROMACS, have you ever use the distance restrain to between the protein and the center of mass of membrane. In gromacs, I can not find the option to choose the center of mass of specific groups like membra