RE: [gmx-users] lipid membrane slicing

2011-10-19 Thread Poojari, Chetan
. From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 17 October 2011 20:25 To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipid membrane slicing Poojari, Chetan wrote

Re: [gmx-users] lipid membrane slicing

2011-10-19 Thread Justin A. Lemkul
Poojari, Chetan wrote: Hi Justin, I used the below g_select command to get the list of phosphorus atoms (from DPPC lipid) within 0.5 nm of protein. g_select -f ordered.xtc -n initial.ndx -on select.ndx -select name P and within 0.5 of group Protein -s md_500ns.tpr -b 10 -dt 1000 My

RE: [gmx-users] lipid membrane slicing

2011-10-17 Thread Poojari, Chetan
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] On Behalf Of Justin A. Lemkul [jalem...@vt.edu] Sent: 14 October 2011 12:44 To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipid membrane slicing Poojari, Chetan wrote: Thank you Justin, Igor for your

Re: [gmx-users] lipid membrane slicing

2011-10-17 Thread Justin A. Lemkul
for GROMACS users Subject: Re: [gmx-users] lipid membrane slicing Poojari, Chetan wrote: Thank you Justin, Igor for your suggestions. I tried with trjorder and below is the command i used: trjorder -f *.xtc -s *.tpr -n order.ndx -na 50 -da 0 -r 0.5 -o ordered.xtc I choose protein as my reference

RE: [gmx-users] lipid membrane slicing

2011-10-14 Thread Poojari, Chetan
:24 To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipid membrane slicing Igor Marques wrote: chetan, i'm not sure about the use of -sl option in g_order. however, for the purpose you mentioned, i'd suggest you to: create two different trajectories, using trjconv and an index

Re: [gmx-users] lipid membrane slicing

2011-10-14 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: 11 October 2011 23:24 To: Discussion list for GROMACS users Subject: Re: [gmx-users] lipid membrane slicing Igor Marques wrote: chetan, i'm not sure about

Re: [gmx-users] lipid membrane slicing

2011-10-11 Thread Justin A. Lemkul
Igor Marques wrote: chetan, i'm not sure about the use of -sl option in g_order. however, for the purpose you mentioned, i'd suggest you to: create two different trajectories, using trjconv and an index file grouping lipids closer to the protein and lipids away from the protein. then, you

Re: [gmx-users] lipid membrane slicing

2011-10-11 Thread lina
On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan c.pooj...@fz-juelich.dewrote: Hi, I have protein completely inserted into lipid membrane and would like to study order parameter around the protein as well as away from the protein. For this I would like to slice my membrane into parts. I