On 7/16/13 5:30 AM, Shima Arasteh wrote:
Hi,
Would you please let me know how can I make an index file of COM of lipid
membrane?
I guess the position of the COM of the bilayer, but how it is possible to make
an index file of this point?
I want to include this index file as the ref_group
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sunday, April 29, 2012 3:10 AM
Subject: Re: [gmx-users] Make an index file
On 4/28/12 2:06 PM, Peter C. Lai wrote:
#2
Generally a good idea to keep the names
On 29/04/2012 7:32 PM, Shima Arasteh wrote:
Actually, I am confused somehow.
I want to equilibrate the system. It contains popc and water. To
equilibrate it, using .mdp file I use the nvt.mdp file as below.
title= NVT equilibration for POPC
define= -DPOSRES; position
Dear MArkWow, That was kind of you.
I appreciate you.
Ok, I will try it.
Thanks,
Shima
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sunday, April 29, 2012 2:11 PM
Subject: Re: [gmx-users] Make
Dear Mark,
Wow, That was kind of you.
I appreciate you.
Ok, I will try it.
Thanks,Shima
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Sunday, April 29, 2012 2:11 PM
Subject: Re: [gmx-users] Make
#2
Generally a good idea to keep the names consistent, however - why are you using
POP in the coordinate file instead of POPC?
--
Sent from my Android phone with K-9 Mail. Please excuse my brevity.
Shima Arasteh shima_arasteh2...@yahoo.com wrote:
Dear gmx users,
I want to simulate POPC in
On 4/28/12 2:06 PM, Peter C. Lai wrote:
#2
Generally a good idea to keep the names consistent, however - why are you using
POP in the coordinate file instead of POPC?
If it is a .pdb file, the standard residue name occupies 3 characters. Many
files (including those from Tieleman) are
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