Dear GROMACS users
I want to analysis of 2 micelles that are created in one simulation, when I
view output of trajectory by vmd or ngmx:
ngmx -f md.trr -s md.tpr
has been created 2 micelles, then I try to micelle clustering by:
1. trjconv -f md.xtc -o a_cluster.gro -e 0.001 -pbc
On 12/24/2011 8:01 PM, mohammad agha wrote:
Dear GROMACS users
I want to analysis of 2 micelles that are created in one simulation,
when I view output of trajectory by vmd or ngmx:
ngmx -f md.trr -s md.tpr
has been created 2 micelles, then I try to micelle clustering by:
1. |trjconv -f
Thank you very much.
Best Regards
Sara
From: Mark Abraham mark.abra...@anu.edu.au
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Saturday, December 24, 2011 1:48 PM
Subject: Re: [gmx-users] micelle clustering
On 12/24/2011 8:01 PM
On 1/07/2011 3:35 PM, sulatha M. S wrote:
Hi Tsjerk,
I installed gromacs myself. I put the modified gmx_trjconv.c code in
the /src/tools subdirectory where the source code is located and tried
the command
make trjconv
But it gives me a series of error messages, as given below.
They're all
Thanks Mark,
I will do the analysis in 4.5.4. Hope while doing the micelle clustering I
will not get into a infinite loop as in 4.0.7.
If I understand correctly, While using trjconv -pbc cluster, I should use
-e 0.002 or the frames (-dump option) in the xtc file (generated after the
micelles
Hi Sulatha,
With my clustering algorithm there can be no infinite loop :)
By the way, sorry for the error messages you ran into with compiling
4.0.7. It had escaped me that these changes were made after that
version.
Cheers,
Tsjerk
On Fri, Jul 1, 2011 at 8:29 AM, sulatha M. S
Hi all,
I have simulated a system of randomly dispersed surfactants in water using
gromacs (4.0.7) for about 100 ns MD. Micelles are formed after around 40 ns.
I am using a time step of 0.002 fs with xtc files written every 500 steps.
For analyzing the micellar properties, I tried the commands
Dear Sulatha,
You can try the command trjconv -f a.xtc -o
b.gro -pbc cluster -e 0.002 with GROMACS 4.5.4.
Best regrds
Grigoris
--- Στις Πέμ., 30/06/11, ο/η sulatha M. S mssula...@gmail.com έγραψε:
Από: sulatha M. S mssula...@gmail.com
Θέμα: [gmx-users] micelle clustering
Προς: Discussion
* έγραψε:
Από: sulatha M. S mssula...@gmail.com
Θέμα: [gmx-users] micelle clustering
Προς: Discussion list for GROMACS users gmx-users@gromacs.org
Ημερομηνία: Πέμπτη, 30 Ιούνιος 2011, 9:18
Hi all,
I have simulated a system of randomly dispersed surfactants in water using
gromacs (4.0.7
Sulatha,
You can try the command trjconv -f a.xtc -o b.gro -pbc cluster -e 0.002with
GROMACS 4.5.4.
Best regrds
Grigoris
--- Στις *Πέμ., 30/06/11, ο/η sulatha M. S mssula...@gmail.com* έγραψε:
Από: sulatha M. S mssula...@gmail.com
Θέμα: [gmx-users] micelle clustering
Προς: Discussion list
10 matches
Mail list logo