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
ds,
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
Pooja
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
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 y
ds, chetan
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
: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 trajec
On Wed, Oct 12, 2011 at 1:20 AM, Poojari, Chetan wrote:
> 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 tried the followi
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 sh
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 should be able to analyse e
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