Re: [gmx-users] Trajectories

2012-06-06 Thread Erik Marklund
Pymol has similar functionality, in case you prefer that over VMD. 5 jun 2012 kl. 22.23 skrev Peter C. Lai: > You can also use something like VMD where you load the trajectory then > select your atoms, then increment the frames and extract the xyz coordinates > of each of your atoms in the selec

Re: [gmx-users] Trajectories

2012-06-06 Thread Erik Marklund
5 jun 2012 kl. 16.52 skrev Thomas Piggot: > Hi, > > I think Erik meant to say that the program is trjorder (not g_order) for the > ordering of molecules by distance. > > Cheers > > Tom Indeed I did. Sorry, and thanks for the correction. Erik > > On 05/06/12 14:41, Erik Marklund wrote: >>

Re: [gmx-users] Trajectories

2012-06-05 Thread Peter C. Lai
You can also use something like VMD where you load the trajectory then select your atoms, then increment the frames and extract the xyz coordinates of each of your atoms in the selection. You can do that in 5 lines of TCL script (just don't update the select within selection after each frame or el

RE: [gmx-users] Trajectories

2012-06-05 Thread Blake Rankin
ot;Justin A. Lemkul" > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] Trajectories > > > On 6/5/12 9:02 AM, rankinb wrote: > > I am interested in pulling out the trajectories (x,y,z coordinates) > > of > water > > molecules within a certai

Re: [gmx-users] Trajectories

2012-06-05 Thread Thomas Piggot
Hi, I think Erik meant to say that the program is trjorder (not g_order) for the ordering of molecules by distance. Cheers Tom On 05/06/12 14:41, Erik Marklund wrote: 5 jun 2012 kl. 15.05 skrev Justin A. Lemkul: On 6/5/12 9:02 AM, rankinb wrote: I am interested in pulling out the traje

Re: [gmx-users] Trajectories

2012-06-05 Thread lloyd riggs
Original-Nachricht > Datum: Tue, 05 Jun 2012 09:05:09 -0400 > Von: "Justin A. Lemkul" > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] Trajectories > > > On 6/5/12 9:02 AM, rankinb wrote: > > I am interested i

Re: [gmx-users] Trajectories

2012-06-05 Thread lloyd riggs
n A. Lemkul" > An: Discussion list for GROMACS users > Betreff: Re: [gmx-users] Trajectories > > > On 6/5/12 9:02 AM, rankinb wrote: > > I am interested in pulling out the trajectories (x,y,z coordinates) of > water > > molecules within a certain distance

Re: [gmx-users] Trajectories

2012-06-05 Thread Erik Marklund
5 jun 2012 kl. 15.05 skrev Justin A. Lemkul: > > > On 6/5/12 9:02 AM, rankinb wrote: >> I am interested in pulling out the trajectories (x,y,z coordinates) of water >> molecules within a certain distance of my solute molecule. I have tried >> using g_select, but that will only give me the atom

Re: [gmx-users] Trajectories

2012-06-05 Thread Justin A. Lemkul
On 6/5/12 9:02 AM, rankinb wrote: I am interested in pulling out the trajectories (x,y,z coordinates) of water molecules within a certain distance of my solute molecule. I have tried using g_select, but that will only give me the atom numbers and not the trajectories. I can create an index fi

[gmx-users] Trajectories

2012-06-05 Thread rankinb
I am interested in pulling out the trajectories (x,y,z coordinates) of water molecules within a certain distance of my solute molecule. I have tried using g_select, but that will only give me the atom numbers and not the trajectories. I can create an index file using this command but unfortunatel

[gmx-users] Trajectories sampling

2006-05-19 Thread Alessandro Mattozzi
Title: Trajectories sampling Hi all I am running diffusion simulation. When collecting my penetrant trajectories, shall I use NPT or NVT dynamics? It looks like references are divided about that... Thank you Regards Alessandro Mattozzi M.Phil., Ph.D. student Dept. of Fibre and Polymer Techno