RE: [gmx-users] input the gro and trr file into the VMD

2009-02-20 Thread Berk Hess
vt.edu; gmx-users@gromacs.org > Date: Fri, 20 Feb 2009 00:38:35 + > Subject: RE: [gmx-users] input the gro and trr file into the VMD > CC: > > Hi, > > I am sorry for that cause every time I sent my question, it shows that this > email was not delivered and hence, I j

RE: [gmx-users] input the gro and trr file into the VMD

2009-02-19 Thread He, Yang
[jalem...@vt.edu] Sent: Thursday, February 19, 2009 2:59 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] input the gro and trr file into the VMD You've posted the same exact question five times today, even though you got a very good response already: http://www.gromacs.org/pipe

Re: [gmx-users] input the gro and trr file into the VMD

2009-02-19 Thread Justin A. Lemkul
You've posted the same exact question five times today, even though you got a very good response already: http://www.gromacs.org/pipermail/gmx-users/2009-February/039830.html If you want free advice, take what you're given, demonstrate that you've made some efforts to solve your problem, and

[gmx-users] input the gro and trr file into the VMD

2009-02-19 Thread He, Yang
Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?

Re: [gmx-users] input the gro and trr file into the VMD

2009-02-19 Thread XAvier Periole
VMD defines the bonds according to a distance criteria. Note that these are not defined in a gro or trr file but in the tpr, which is not red by VMD. If your distances are not seen this means that the atoms are not within the VMD's criteria. Are you using a CG model where the distances are la

[gmx-users] input the gro and trr file into the VMD

2009-02-19 Thread He, Yang
Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?

[gmx-users] input the gro and trr file into the VMD

2009-02-18 Thread He, Yang
Hi all users, When I try to input the .gro and .trr file into the VMD, I always find that there is no bond connected among the atoms.But in fact, I have defined all the bond connection in the gromacs files. Can anyone tell me how to get the snap shots in the VMD with the bonds among the atoms?