Hi,
in addition to Chris' comments, I think one good way for getting APL of
a lipid mixture is the one proposed by Edholm and Nagle :
http://www.cell.com/biophysj/abstract/S0006-3495%2805%2972827-7.
The idea is to run simulations at different concentrations of [A] and [B].
Ciao,
Patrick
Le
Hi,
I am trying to understand what is the difference between g_rms and
g_rmsdist commands.
I have looked at the manual and all I can find is that:
*g_rms*: The root mean square deviation (RM SD) of certain atoms in a
molecule with respect to a reference
structure can be calculated with the
Hi,
In CHARMM I generated a short peptide. The N-terminal is a regular
-NH2 (patch NNEU) while the C-terminal is amidated (patch CT2).
I would like to import the PDB to GROMACS using pdb2gmx by using the
CHARMM27 forcefield later. I issue the following command:
pdb2gmx -v -f irik-l.pdb
Hi,
You indeed could use the g_rdf command like this (in the script)
g_rdf_mpi -f $pathXTC -s $pathTPR -n bOG_Micelle_RDF.ndx -norm -com -b
$timeBegin1 -e $timeEnd1 -o $name1_$name2_$name3_$i_original.xvg
RadDensFunc_$i.txt
Where in the RadDensFunc.txt file, i choose as the first group the
On 5/10/13 12:35 AM, Arunima Shilpi wrote:
Hello sir
As in the tutorial for umbrella sampling command
make_ndx -f npt.gro
you have selected two different groups as Chain_A as 19 and Chain_B as 20
If we have protein-ligand interaction whether we should have single group
of protein-ligand
On 5/10/13 1:55 AM, Shima Arasteh wrote:
Hi,
In Umbrella Sampling method, among mdp settings, there is a section where the
pull code settings are defined in:
pull = umbrella: using a harmonic potential to pull
As it is said that with US the path of the permeating ion along thereaction
On 5/10/13 4:24 AM, Nawel Mele wrote:
Hi,
I am trying to understand what is the difference between g_rms and
g_rmsdist commands.
I have looked at the manual and all I can find is that:
*g_rms*: The root mean square deviation (RM SD) of certain atoms in a
molecule with respect to a reference
On 5/10/13 5:16 AM, Jernej Zidar wrote:
Hi,
In CHARMM I generated a short peptide. The N-terminal is a regular
-NH2 (patch NNEU) while the C-terminal is amidated (patch CT2).
I would like to import the PDB to GROMACS using pdb2gmx by using the
CHARMM27 forcefield later. I issue the
Hi,
Thank you very much from your answer, but I think this is about numerical
density (g(r)*(N/V)) or mass density (g(r)*(m/V))?
I want to know about probability(nm^-1) with g_rdf, Please?
Best Regards
Sara
- Forwarded Message -
From: ABEL Stephane 175950 stephane.a...@cea.fr
To:
hello everyone
I am trying to cluster my data using g_cluster.I simulated the whole
protein. I did the g_cluster analysis with only certain region of the
protein which I specified using an index file.The program runs fine and
gives 1 cluster.My concern is the warning it gives which states that :-
Dear gmx members,
I have posted the same question previously , but I didn't get any reply.
So, if anyone can help me out ...
I performed a REMD simulation on a peptide 384 atoms (24 residues). In
total 11 replicas were simulated for a period of 50ns each. The exchange
was allwoed at every 1000
The replicas seem indeed to have exchange. Using a colour for the # replicas
would help.
I could not access to the first link.
Note also that the increase of exchange ratio with the temperature suggest the
distribution of the temperature is not optimal and may be with regular
intervals? You
Hi,
Thank you very much from your answer, but I think this is about numerical
density (g(r)*(N/V)) or mass density (g(r)*(m/V))?
I want to know about probability(nm^-1) with g_rdf, Please?
Best Regards
Sara
- Forwarded Message -
From: ABEL Stephane 175950 stephane.a...@cea.fr
To:
Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the
output is printed on the terminal, but I want them into a file as separately.
May I ask you to help me, Please?
Thank you in advance
Best Regards
Sara
--
gmx-users mailing list
On 5/10/13 11:27 AM, mohammad agha wrote:
Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist, the
output is printed on the terminal, but I want them into a file as separately.
May I ask you to help me, Please?
Redirect the terminal output
Dear Justin,
Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!
Best Regards
Sara
On 5/10/13 11:27 AM, mohammad agha wrote:
Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along
Dear Justin,
Thank you very much from your help.
Best Regards
Sara
On 5/10/13 11:27 AM, mohammad agha wrote:
Dear GROMACS Specialists,
I have one problem with g_dist. When I use g_dist along with option -dist,
the output is printed on the terminal, but I want them into a file as
Hi,
Such an issue typically indicates a GPU kernel crash. This can be
caused by a large variety of factors from program bug to GPU hardware
problem. To do a simple check for the former please run with the CUDA
memory checker, e.g:
/usr/local/cuda/bin/cuda-memcheck mdrun [...]
Additionally, as
On 5/10/13 11:46 AM, mohammad agha wrote:
Dear Justin,
Thank you very much from your answer.
May I ask you to help me more, Please?
I work with UBUNTU, I don't know how should I do it!
Apply Google. This is not a Gromacs issue and should be investigated and
studied in the appropriate
I was trying to install gromacs 4.6.1 with CUDA and have a weird problem.
My system is as the following
new iMAC OS x 10.8.3
GPU : FTX 650 M 512 MB
I also installed the open-mpi libraries into the /usr/local/lib folder
before installation. I have got to say I'm by no means a UNIX expert.
Hi guys, I'm new to Gromacs and seeking some input on my .mdp file for the
production run. I want to perform simulation to check protein stability over
time and the after that the stable protein will be used for protein-protein
docking/interactions. I'm using cubic box (with 1nm pbc) with water
The lack of line-wrapping makes it a pain to read. It happens to my emails that
are posted on this list
(and I have seen others), unless I put explicit line-breaks in my posts, which
I often forget to do.
Is there anything that can be done?
IMHP, this should be automatically handled, and I
Respected Sir
Presently my work includes umbrella sampling for protein ligand
interaction. The components of md_pull.mdp is
title = Umbrella pulling simulation
define = -DPOSRES_B
; Run parameters
integrator = md
dt = 0.002
tinit = 0
nsteps = 25; 500 ps
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