Dear users,
I want to study ion conduction through a protein-memrane system.
First of all, I tried to simulate a usual protein-membrane system. I'd like to
know if it is possible to add asymmetrical number of ions to leaflets of
membrane?
Secondly, is it possible to apply an external
A pdb file with a resid exceeds the proper PDB format.
You can resolvate a dry lipid bilayer using genbox fine; I don't know what
problem you have with the solvation and minimization using that method,
http://manual.gromacs.org/current/online/genbox.html
You can also pdb2gmx or editconf
On 2012-10-01 11:16:43PM -0700, Shima Arasteh wrote:
Dear users,
I want to study ion conduction through a protein-memrane system.
First of all, I tried to simulate a usual protein-membrane system. I'd like
to know if it is possible to add asymmetrical number of ions to leaflets of
Hi Shima,
there is also a patch for Gromacs available to study ion conduction through
membrane channels that you might find useful. Please take a look at this page:
http://www.mpibpc.mpg.de/grubmueller/compel
Best,
Carsten
On Oct 2, 2012, at 8:16 AM, Shima Arasteh
Thanks Casten.
Sincerely,
Shima
- Original Message -
From: Carsten Kutzner ckut...@gwdg.de
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Tuesday, October 2, 2012 11:02 AM
Subject: Re: [gmx-users] Ion conduction
Thanks Peter for your explanation.
Sincerely,
Shima
- Original Message -
From: Peter C. Lai p...@uab.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Tuesday, October 2, 2012 10:10 AM
Subject: Re: [gmx-users] Ion conduction through a protein-membrane system
Hi Justin,
I used ~20 windows to sample ~2 nm pulling. I notice that the distance between
the complex being increased during the pulling but not gradually. At the
distance of 0-1nm, there are 70 snapshots (the distance sometime increased
sometimes decreased). At the distance of 1-2nm, there
On 10/2/12 1:40 AM, Ladasky wrote:
I have been trying to automate my simulation setup and monitoring. I wrote a
script which calls g_energy, and automatically generates plots of potential
energy from my EM step, temperature from my NVT equilibration step, and
pressure and density from my NPT
Hi everybody,
I am still in confusion in which thermostat my be good for
NPT MD calcualtions with protein and DNA. V-rescale, berenseden, Nose-hoover;
parinello-rahman thermostats. Is the temperature and pressure coupling will be
similar or different.
Thanking in advance,
On 10/2/12 5:20 AM, Anik Sen wrote:
Hi everybody,
I am still in confusion in which thermostat my be good for
NPT MD calcualtions with protein and DNA. V-rescale, berenseden, Nose-hoover;
parinello-rahman thermostats. Is the temperature and pressure coupling will be
Dear gmxusers,
Thank you for your answers so far. I have run a few more test rerun and here
is what I got:
-The number of degree of freedom are the same whatever the topology I run
with, both in the log file and from the grompp output.
-Comparing the trajectories created from rerun with
On 10/2/12 4:39 AM, Du Jiangfeng (BIOCH) wrote:
Hi Justin,
I used ~20 windows to sample ~2 nm pulling. I notice that the distance between the
complex being increased during the pulling but not gradually. At the distance of
0-1nm, there are 70 snapshots (the distance sometime increased
Dear All,
Does anyone have a small script for converting Gromacs (GROMOS type) ff to
CHARMM format, or an amino acid top file in CHARMM format for such. I have
seen some scripts, but they work only with different topology types. Thought I
would ask, otherwise I sit here for three days
Hi,
I have tried to simulate a protein in water with the CHARMM27 force field and
the GROMACS simulation package. Without the CMAP correction the simulation runs
just fine, but when adding the CMAP correction to the dihedrals, the protein
quickly starts to unfold and the simulation stops (with
Hello Gromacs users,
The solution that ended up working is selecting a different pull_pbcatom0
from the reference group, the protein, such that the atom is approx. in the
center of mass of the protein.
I hope that others may find this useful,
Thanks to Martin Vesper and Justin Lemkul for their
Dear Friends,
Gromacs script such as g_cluster takes lot of time to complete in a
single machine. Is their any way to give this job to a cluster machine
like mdrun. Since mdrun is MPI enabled so I can easily execute it on
cluster.
Anybody in group have any clue that how we can execute g_cluster
Hi...
you have to implement the algorithm using parallel paradigma (MPI, openmp,
thread)
Alternatively, there is a workaround to bypass the serial rmsd matrix
building (the most
time consuming part).
g_cluster reads a rmsd matrix as input, you can run different rmsd instance
in parallel,
using
On 02/10/12 11:53, Justin Lemkul wrote:
Note that you can always select by name rather than number, i.e.:
echo Temperature | g_energy -f ener.edr
Didn't know that, this really saves me a lot of trouble! Thanks Justin!
m.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
--
gmx-users
On 10/2/12 7:07 AM, rama david wrote:
Hi Gromacs Users,
I did simulation of two random coil peptides for 100ns.
after 70 ns these peptide get converted to anti parallel beta sheet
structure.
I am interested to see the water density in between these peptideswith
respect
hello guys:
I am using g_helixorient to analyze the helix property in my system
and it generate three theta[1,2,3].xvg file. I am wondering what's
that? I didn't find any comments in the help file.
thanks
Albert
--
gmx-users mailing listgmx-users@gromacs.org
On 10/2/12 11:13 AM, Albert wrote:
hello guys:
I am using g_helixorient to analyze the helix property in my system and it
generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find
any comments in the help file.
Have you read the last paragraph of g_helixorient -h?
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But grompp (before minimization of system_inflated.gro) giving error like
this..
Fatal error:
Atomtype LC3 not found
Actually what changes I should do on the system topology, before grompp?
I found that atomtype LC3
On 10/2/12 11:26 AM, Shine A wrote:
Sir,
I am studying the dynamics of membrane proteins using KALP-15 in DPPC.
But grompp (before minimization of system_inflated.gro) giving error like
this..
Fatal error:
Atomtype LC3 not found
Actually what changes I should do on the system topology,
On 10/02/2012 05:16 PM, Justin Lemkul wrote:
On 10/2/12 11:13 AM, Albert wrote:
hello guys:
I am using g_helixorient to analyze the helix property in my
system and it
generate three theta[1,2,3].xvg file. I am wondering what's that? I
didn't find
any comments in the help file.
Have
On 10/2/12 11:35 AM, Albert wrote:
On 10/02/2012 05:16 PM, Justin Lemkul wrote:
On 10/2/12 11:13 AM, Albert wrote:
hello guys:
I am using g_helixorient to analyze the helix property in my system and it
generate three theta[1,2,3].xvg file. I am wondering what's that? I didn't find
any
IC.
thanks a lot for kind comments.
On 10/02/2012 05:38 PM, Justin Lemkul wrote:
On 10/2/12 11:35 AM, Albert wrote:
On 10/02/2012 05:16 PM, Justin Lemkul wrote:
On 10/2/12 11:13 AM, Albert wrote:
hello guys:
I am using g_helixorient to analyze the helix property in my
system and
Dear all!
Recently I've forced with the same problem as was in this topic :)
I have tieleman's lipids consisted of 128 dppc with water.
also I have system with the protein inserted in the same bilayer
I wounder to know
1- How I could change lipid number in the pure lipid bilayer (
increase up
On 10/2/12 2:16 PM, James Starlight wrote:
Dear all!
Recently I've forced with the same problem as was in this topic :)
I have tieleman's lipids consisted of 128 dppc with water.
also I have system with the protein inserted in the same bilayer
I wounder to know
1- How I could change lipid
On 10/2/12 12:49 PM, Edward Deira wrote:
Dear all,
From the computational side of the question, can one compare the final
energy values at the end of a simulation ? Are those energy values are
meaningful ?
Can I, with proper chemical judgement, say that a lower (more negative)
value will
not that off-base, actually. one of my aims is to compare two different
proteins with the same ligand and try to figure out which system is
energetically more favourable without having to go through qm/mm. so i
suppose the proper way would be estimating the absolute free energy of
the system.
can
Justin,
I've done exactly like you provide me ( changing only x and y )
but in that case the protein and the old lipids were slightly shifted
to one side of the new system. Is there any way to center the old
system in respect to the new solvent ?
Also I've noticed that when I increase size of
On 10/2/12 2:56 PM, James Starlight wrote:
Justin,
I've done exactly like you provide me ( changing only x and y )
but in that case the protein and the old lipids were slightly shifted
to one side of the new system. Is there any way to center the old
system in respect to the new solvent ?
On 10/2/12 2:45 PM, Edward Deira wrote:
not that off-base, actually. one of my aims is to compare two different
proteins with the same ligand and try to figure out which system is
energetically more favourable without having to go through qm/mm. so i
suppose the proper way would be estimating
Justin
Previously I've expanded initial system on Z-dim before the protein
was inserted to increase both water layers.
After current processing with Genbox there is no problems in Z
actually- it look likes sandwich with two broader bread layers and
narrower cutlet :) So the lipid layer in x and
On 10/2/12 3:49 PM, James Starlight wrote:
Justin
Previously I've expanded initial system on Z-dim before the protein
was inserted to increase both water layers.
After current processing with Genbox there is no problems in Z
actually- it look likes sandwich with two broader bread layers and
This is exactly what I've obtained
http://imageshack.us/photo/my-images/27/89293914.png/
the same effect was also in case of intact tieleman's lipid bilayers (
the water layers were broader than lipid after resizing with genbox)
James
2012/10/2, Justin Lemkul jalem...@vt.edu:
On 10/2/12
Hi,
I'm using the pull code to maintain the initial structure of a protein
that otherwise deforms. Using pull=umbrella does what I expect it to,
but pull=constraint produces zero forces. I'm using version 4.5.5 with
the MARTINI force field.
The pull=umbrella mdp contains the following,
and
Justin Lemkul wrote
Note that you can always select by name rather than number, i.e.:
echo Temperature | g_energy -f ener.edr
That's undocumented, as of the GROMACS 4.5.4 manual, but VERY useful.
Thanks.
--
View this message in context:
On 10/2/12 4:12 PM, James Starlight wrote:
This is exactly what I've obtained
http://imageshack.us/photo/my-images/27/89293914.png/
This looks completely normal. What I was asking for was an image of one of your
failed attempts that has whatever odd manifestation you've been trying to
Dear Gromacs users,
I am trying to find inter atomic distances between ligand atoms and
protein residues using Gromacs commands and could generate individual
xvg files, but could not figure out how to merge or show all the xvg
files in one graph using xmgrace.
Cold you please suggest?
Thanks
Dear Pramod
use the command
xmgrace -nxy file1.xvg file2.xvg
Instead of file1 and file2 use ur file name.
On Tue, Oct 2, 2012 at 8:49 PM, ram bio rmbio...@gmail.com wrote:
Dear Gromacs users,
I am trying to find inter atomic distances
Thank you Justin for your reply ,
I tried g_density again after your reply. But I found that
it give density with respect to box dimension and not to time.
g_densmap have xpm output and no the xvg ( I need density or no of water
molecule present in between two peptides with respect to the time
Hi.
Thanks for the tip. I turned the problem was caused by the PDB file.
It seems the water segment was not written properly (starting with
residue 1 and then all the way to the last one). After correcting this
and then manually editing the new PDB file to change the atom names
from TIP3 to SPCE
Justin,
I've told about lower lipid density at the left and right edges of the
new system ( see new pic bellow with marked regions).
http://imageshack.us/photo/my-images/10/dppc.png/
I've started with system consisted of 118 lipids and 6000 water in dims 6x6x10
I've created new box with the
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