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 2011-12-24 12:20, Su Nh wrote:
Dear all
I used PRODRG to build the topology file of a ligand (GROMOS force
field). Now I want to calculate the partial charges with Gaussian, but I
do not know whichbasis set and method I have to use to be compatible
with GROMOS. Could you please help me?
To whom it may concern;
I am willing to study a damaged DNA which has a 8-oxoG as the lesion (the
Carbon 8 in guannine is oxidized.). I have the following questions;
1) Should I change the sigma and epsilon parameters in the force field that I
want to work on? and how?
2) Should I change the
Dear gromacs users
I would like to calculate the standard deviation (as the error bar) for
rmsd.xvg file.
If rmsd.xvg was used in excel software, it gives a graph as rmsd vs time. I
want to have a file containing rmsd vs time
and error bar relating to rmsd values such that after plotting by
--- On Sat, 12/24/11, banafsheh mehrazma bmehra...@yahoo.com wrote:
From: banafsheh mehrazma bmehra...@yahoo.com
Subject:
To: gmx-users@gromacs.org
Date: Saturday, December 24, 2011, 3:39 AM
To whom it may concern;
I am willing to study a damaged DNA which has a 8-oxoG as the lesion
Dear gromacs users
In the average file, there are 3 columns:
first column is time, second is rmsd value.
third column is 0.
what is third column?
best regards.
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
On 12/24/2011 10:41 PM, banafsheh mehrazma wrote:
--- On *Sat, 12/24/11, banafsheh mehrazma /bmehra...@yahoo.com/* wrote:
From: banafsheh mehrazma bmehra...@yahoo.com
Subject:
To: gmx-users@gromacs.org
Date: Saturday, December 24, 2011, 3:39 AM
To whom it may concern;
On 12/24/2011 10:40 PM, leila karami wrote:
Dear gromacs users
I would like to calculate the standard deviation (as the error bar)
for rmsd.xvg file.
If rmsd.xvg was used in excel software, it gives a graph as rmsd vs
time. I want to have a file containing rmsd vs time
and error bar
Dear Mark
Thanks for your quick reply.
For what parameters I can use g_analyze -av average.xvg -errbar stddev -f
*.xvg?
Can I use above tool for obtaining error bars for a *.xvg file resulting
from g_dist?
--
gmx-users mailing listgmx-users@gromacs.org
On 2011-12-24 13:08, Su Nh wrote:
Dear Prof. van der Spoe
Thank you for your responce. But I want to know if the charges in the
topology files, which are built by ATB, are accurate and there is no
need to re-calculate them or not?
On the oder hand, what is the compatible parameters (basis set
Dear All,
When I try to run Benzene Simulation I am getting following
error after the grompp for energy minimization.
ERROR 1 [file benz.top, line 115]:
No default Proper Dih. types
ERROR 2 [file benz.top, line 116]:
No default Proper Dih. types
ERROR 3 [file benz.top, line
Dear all
I used PRODRG to build the topology file of a ligand (GROMOS force field). Now
I want to calculate the partial charges with Gaussian, but I do not know which
basis set and method I have to use to be compatible with GROMOS. Could you
please help me?
Thanks--
gmx-users mailing
Su Nh wrote:
Dear all
I used PRODRG to build the topology file of a ligand (GROMOS force
field). Now I want to calculate the partial charges with Gaussian, but I
do not know which basis set and method I have to use to be compatible
with GROMOS. Could you please help me?
Dear Mark;
Thank you for your instant reply. You are right, but in my case, there is a
residue 8-OxoG (oxidized G). As you know, in all of the force fields in
Gromacs package, G,C,A and T are known. In your opinion, what should I do in
case of 8-OxoG, to obtain parameters needed for this new
On 12/25/2011 6:04 PM, banafsheh mehrazma wrote:
Dear Mark;
Thank you for your instant reply. You are right, but in my case, there
is a residue 8-OxoG (oxidized G). As you know, in all of the force
fields in Gromacs package, G,C,A and T are known. In your opinion,
what should I do in case
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