Hi everyone,
when am doing this g_dist between the protein and water am getting the
distance between water-water. why it is so?? and is there a way i can find
distance in each time frame.
Thanks
On Thu, Sep 8, 2011 at 5:55 PM, aiswarya pawar aiswarya.pa...@gmail.comwrote:
Hi users,
To get
gmx-users@gromacs.org
Dear Gmx users,
I am working on a transmembrane protein and my system contains protein, DPPC
bilayer, water (spc) and ions. After preparing my system for simulation I
have successfully performed the energy minimization, I am facing a problem
at the nvt equilibration phase
Hi Users,
Am using g_dist to find the distance between water and protein. but my
output has the values of SOL-water distance.
t: 1 136 SOL 2336 OW 0.772373 (nm)
Thanks
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Please search the
Hi gmx-users,
I am trying to a study of GLA domain simulation in membrane by using coarse
gained models. There is a problem coming from converting all-atom model to
coarse gained because GLA domain contains some unusual residues (10 glutamate
residues were modified by carboxylation) and also
Message: 1
Date: Sun, 11 Sep 2011 13:01:28 +0200
From: gal.fra...@live.biu.ac.il
Subject: [gmx-users] g_lie
To: gmx-users@gromacs.org
Message-ID: blu160-w601d2ab913084c46676afee9...@phx.gbl
Content-Type: text/plain; charset=windows-1255
Greetings to all!
I have a question for the g_lie
Lloyd thank you very much for your answer!
I'm going to check it out...
Best regards,
Gal
Date: Mon, 12 Sep 2011 10:34:59 +0200
From: lloyd.ri...@gmx.ch
To: gmx-users@gromacs.org
Subject: [gmx-users] RE:g_lie
Message: 1
Date: Sun, 11 Sep 2011 13:01:28 +0200
From:
Dear Gmx users,
I am working on a transmembrane protein and my system contains protein, DPPC
bilayer, water (spc) and ions. After preparing my system for simulation I
have successfully performed the energy minimization, I am facing a problem
at the nvt equilibration phase of 100ps, the lipid
Sir, thanks for your reply
Yes I should have limited number of structure for a given point(pc1,pc2) but
in my case, I have taken pc1 and pc2 as a range of points where the
minima in FEL lies rather than a
single point.So I think it would be relevant to apply the clustering
as per your
Parul tew wrote:
Dear Gmx users,
I am working on a transmembrane protein and my system contains protein, DPPC
bilayer, water (spc) and ions. After preparing my system for simulation I
have successfully performed the energy minimization, I am facing a problem
at the nvt equilibration phase of
aiswarya pawar wrote:
Hi everyone,
when am doing this g_dist between the protein and water am getting the
distance between water-water. why it is so?? and is there a way i can
find distance in each time frame.
The distance is calculated based on the groups you tell g_dist to analyze.
aiswarya pawar wrote:
Hi Users,
Am using g_dist to find the distance between water and protein. but my
output has the values of SOL-water distance.
t: 1 136 SOL 2336 OW 0.772373 (nm)
This is not a water-water distance, it is the output of the -dist option telling
you that water
Hi gromacs Users,
Am using g_dist to find the distance between water and protein. for
that i made a index file such as-
a CA(protein atoms)
a OW(water atoms)
i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
instead of getting the result for protein-SOL distance .
aiswarya pawar wrote:
Hi gromacs Users,
Am using g_dist to find the distance between water and protein. for that i made
a index file such as-
a CA(protein atoms)
a OW(water atoms)
i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
instead of getting the
Hi Justin,
Am using g_dist to find the distance between water and protein. for
that i made a index file such as-
a CA(protein atoms)
a OW(water atoms)
i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
instead of getting the result for protein-SOL distance . my
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.
Thanks
On Mon, Sep 12, 2011 at 4:49 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi Users,
Am using g_dist to find the
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be distance
between the SOL protein atoms, instead it is SOL water atoms.
Thanks
On Mon, Sep 12, 2011 at 4:53 PM, Justin A. Lemkul jalem...@vt.edu wrote:
aiswarya pawar wrote:
Hi gromacs Users,
Am using g_dist to
aiswarya pawar wrote:
Hi Justin,
Am using g_dist to find the distance between water and protein. for that i made
a index file such as-
a CA(protein atoms)
a OW(water atoms)
i then run this cmd- g_dist -f md.xtc -s md.tpr -n index.ndx -e 500 -dist 0.35
instead of getting the result for
aiswarya pawar wrote:
hi Justin,
As far i referred the OW,HW1 etc are water atoms so how can it be
distance between the SOL protein atoms, instead it is SOL water atoms.
The printed distance indicates that there is a certain water molecule that is
just over 2 hydrogen bonding lengths
Hi,
I am confused, why the job is running,
but they did not write the .edr, .log .xtc ... files.
Everything showed so normal, just not writing,
when I used thread, all is fine, the writing is normal.
just use mpi, I tried different nodes, still not work, now two hours later,
still no writing,
Dear Gromacs users,
I am currently working on porting forcefields from Gromacs to another
program with the aim of simulating DNA. Therefore, I wrote a little
script which reads in a PDB file, evaluates the Lennard-Jones and the
Coulomb energy in vacuo with the forcefield data from Gromacs. I
lina wrote:
Hi,
I am confused, why the job is running,
but they did not write the .edr, .log .xtc ... files.
Everything showed so normal, just not writing,
when I used thread, all is fine, the writing is normal.
just use mpi, I tried different nodes, still not work, now two hours
later,
On 12/09/2011 10:23 PM, lina wrote:
Hi,
I am confused, why the job is running,
but they did not write the .edr, .log .xtc ... files.
Everything showed so normal, just not writing,
when I used thread, all is fine, the writing is normal.
just use mpi, I tried different nodes, still not work,
Matthias Ernst wrote:
Dear Gromacs users,
I am currently working on porting forcefields from Gromacs to another
program with the aim of simulating DNA. Therefore, I wrote a little
script which reads in a PDB file, evaluates the Lennard-Jones and the
Coulomb energy in vacuo with the forcefield
On Mon, Sep 12, 2011 at 8:33 PM, Justin A. Lemkul jalem...@vt.edu wrote:
lina wrote:
Hi,
I am confused, why the job is running,
but they did not write the .edr, .log .xtc ... files.
Everything showed so normal, just not writing,
when I used thread, all is fine, the writing is normal.
On Mon, Sep 12, 2011 at 8:35 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 12/09/2011 10:23 PM, lina wrote:
Hi,
I am confused, why the job is running,
but they did not write the .edr, .log .xtc ... files.
Everything showed so normal, just not writing,
when I used thread, all is
Dear all,
In an attempt to simulate the effect of adding calcium ion to the solvent
around my protein of interest, I wonder how to add Ca2+ ions in the
following cases (in GROMACS 4.5.4):
1) adding Ca2+ ions randomly distributed in the solvent;
2) adding Ca2+ such that it is initially
Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt trajectory
and one mutant trajectory using the following command:
g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
wt_backbone.ndx
The file wt_backbone.ndx contains the backbone of the protein (Backbone
indices
Shay Teaching wrote:
Hi all,
(Gromacs 4.0.7): I am trying to make rms matrix between one Wt
trajectory and one mutant trajectory using the following command:
g_rms -f wt.xtc -f2 mutant.xtc -s wt.tpr -m -fit rot+trans -n
wt_backbone.ndx
The file wt_backbone.ndx contains the backbone of
When I try to work the command on a small portion of the backbone it seems
to work just fine. But when I try the entire backbone (which is composed of
several *separate* chains) I am getting segmentation fault.
Any workaround for that, so I can use the entire backbone?
Thanks again,
-Shay
On Mon,
Shay Teaching wrote:
When I try to work the command on a small portion of the backbone it
seems to work just fine. But when I try the entire backbone (which is
composed of several _separate_ chains) I am getting segmentation fault.
Any workaround for that, so I can use the entire backbone?
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--
Message: 2
Date: Mon, 12 Sep 2011 21:12:26 +0800
From: lina lina.lastn...@gmail.com
Subject: Re: [gmx-users] How do I examine the results didn't
Hi Guys,
I want to run a protein which contains some carboxylated residues into a
membrane. I have had to add a special residue into itp file since there is no
any description in normal itp for GLA residue. I admit some values I added for
GLA residue were ambiguous because I don't know the
Du Jiangfeng (BIOCH) wrote:
Hi Guys,
I want to run a protein which contains some carboxylated residues into a
membrane. I have had to add a special residue into itp file since there is no
any description in normal itp for GLA residue. I admit some values I added for
GLA residue were
Hi Gmx users,
Are we able to run both the lower and higher version at a time?
If possible, please help me how to do it.
with thanks
***+
Dr.Karunakaran Chandran+
Biophysics Department +
Medical College of Wisconsin +
Milwaukee,
On Mon, 2011-09-12 at 21:57 +0530, chandran karunakaran wrote:
Hi Gmx users,
Are we able to run both the lower and higher version at a
time?
If possible, please help me how to do it.
with thanks
You can always run different instances of a program at the same time. As
you
Hi all,
I am not a CS person, but I did find something in acpype.py as
.
if phase in [0, 180]:
properDihedralsGmx45.append([item[0].atoms, phaseRaw,
kPhi, period])
if not self.gmx45:
if kPhi 0: V[period]
Thanks, I'll try that, and post again if it works.
On Mon, Sep 12, 2011 at 6:20 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Shay Teaching wrote:
When I try to work the command on a small portion of the backbone it seems
to work just fine. But when I try the entire backbone (which is
Does anyone has a clear definition or a reference for the Twin-range cut-off? I
searched the internet and looked at the manual yet I couldn't get the idea
Thanks Rabab Toubar
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search
On 13/09/2011 6:21 AM, Yun Shi wrote:
Hi all,
I am not a CS person, but I did find something in acpype.py as
.
if phase in [0, 180]:
properDihedralsGmx45.append([item[0].atoms,
phaseRaw, kPhi, period])
if not self.gmx45:
On 13/09/2011 8:56 AM, Rabab Toubar wrote:
Does anyone has a clear definition or a reference for the Twin-range cut-off? I
searched the internet and looked at the manual yet I couldn't get the idea
Manual 4.6.3 and 3.4.7, and the top hits from Googling twin-range
cutoff look pretty
Rabab Toubar wrote:
Does anyone has a clear definition or a reference for the Twin-range cut-off? I
searched the internet and looked at the manual yet I couldn't get the idea
A twin-range cutoff just means that your short-range cutoffs aren't all the same
value, such that they form two
On 13/09/2011 12:03 AM, m r wrote:
Dear all,
In an attempt to simulate the effect of adding calcium ion to the solvent
around my protein of interest, I wonder how to add Ca2+ ions in the
following cases (in GROMACS 4.5.4):
1) adding Ca2+ ions randomly distributed in the solvent;
genion does
Dear all,
Is there any function to get the Volume around a peptide/protein as a
function of R?
The problem is g_rdf -surf doesn't have a volume correction factor, so my
aim is to apply a volume correction factor manually by having V(R) around
the protein.
Thanks,
--
Elif Nihal Korkmaz
On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote:
Dear all,
Is there any function to get the Volume around a peptide/protein as a
function of R?
The problem is g_rdf -surf doesn't have a volume correction factor, so
my aim is to apply a volume correction factor manually by having V(R)
around
R is any distance from the surface of the protein.
On Mon, Sep 12, 2011 at 6:31 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 13/09/2011 9:29 AM, E. Nihal Korkmaz wrote:
Dear all,
Is there any function to get the Volume around a peptide/protein as a
function of R?
The problem is g_rdf
And I don't think g_sas would do what i want. It calculates the volume of
the protein itself. I am interested in the V of space at a distance R from
the surface of the protein, excluding the volume of the protein. In other
words, i need the surface accessible volume as a function of distance from
On 13/09/2011 9:47 AM, E. Nihal Korkmaz wrote:
And I don't think g_sas would do what i want. It calculates the volume
of the protein itself. I am interested in the V of space at a distance
R from the surface of the protein, excluding the volume of the
protein. In other words, i need the
Dear all，
To make molecules move, accelerate should be used. nstcomm is the frequency for
center of mass motion removal
But if they are used together, the molecule will not move.
I made a model system: a box of pure water. Adding accelerate to SOL in Z
direction.
Firstly, comm_mode was set
Hi everyone,
I'm trying to implement time-varying charges for various ions located
in ions.itp in GROMACS 4.5.4, but I'm not sure where to begin.
I've already had some luck implementing AC external electric fields by
modifying /src/mdlib/sim_util.c, but this required minimal work from
me and a
Dear Gmx users
I have run MD on carbon nanotube with solvated drug molecules inside and
outside the tubes. Kindly would you please let me know how I
can visualize and calculate the amount of molecules only inside the carbon
nanotube during MD process. May I know what keywords I should use in graph
Even if I specify an atom say 1277 atom number to find distance against the OW
atoms. I get the same result of SOL-OW distance. Is it a bug cause even after
specifying one atom from a protein why doesn't it give me the result for the
SOL.
Thanks
Sent from my BlackBerry® on Reliance Mobile,
aiswarya.pa...@gmail.com wrote:
Even if I specify an atom say 1277 atom number to find distance against the OW
atoms. I get the same result of SOL-OW distance. Is it a bug cause even after
specifying one atom from a protein why doesn't it give me the result for the
SOL.
As was suggested
Iam -dist option because I need the distance between two groups, excluding
-dist gives me X,Y,Z output which I don't want. And am not specifying an -o.
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!
-Original Message-
From: Justin A. Lemkul
Sir, thanks for your reply
Yes I should have limited number of structure for a given point(pc1,pc2) but
in my case, I have taken pc1 and pc2 as a range of points where the
minima in FEL lies rather than a
single point.So I think it would be relevant to apply the clustering
as per your
On 10/09/2011 10:23 AM, Sandeep Somani wrote:
Hi Mark
It worked ! pdb2gmx is now properly processing the pdb, and moreover
the potential energy from gmx is within 1.27 kJ/mol of that from
Charmm. More on energy comparison shortly.
However, further tinkering of the rtp and pdb file was
On 13/09/2011 2:27 PM, aiswarya.pa...@gmail.com wrote:
Iam -dist option because I need the distance between two groups
That is not what g_dist -dist does. Please read g_dist -h.
excluding -dist gives me X,Y,Z output which I don't want.
And other output which you do, but you have to use
Hi all,
I am trying to use the g_membed tool to insert my protein into a DMPC membrane.
My protein is a dimer and hence I separated the two monomers by a TER card in
the original pdb file before pdb2gmx step for gromacs to identify it as teo
separate entities.. I then merged my protein file
Hi Mark,
The -dist option says- print all the atoms in group 2 that are closer than a
certain distance to the center of mass of group 1.
That means it should give me the distance from OW to protein atom.
And when am already specifying only one atom from protein ie say 1322. why
do i get this
On 13/09/2011 3:40 PM, aiswarya pawar wrote:
Hi Mark,
The -dist option says- print all the atoms in group 2 that are closer
than a certain distance to the center of mass of group 1.
That means it should give me the distance from OW to protein atom.
If you choose correct groups that are
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