Hi Emily,
I have no idea about your problems, but I noticed that the gromacs you
used might be the one my colleague had sent to you, he modified
something to fit my multicores processors, I guess you may do a try to
use the original and official one also.
Good luck,
Lina
hi all
i have done protein protein interaction and the complex structure
was taken for MD simulation using Gromacs.while performing mdrun step for
position restrain i got error. i have carried out mdrun for 1ps and the
command given for mdrun
and position restrain are
grompp -f
Dear All,
I recentlly started using Gromacs again. I was just woundering if anyone had
some .rtp libraries available to add on to the software, or for VMD.
I am particularly interested in lipid .rtp libraries hopefully for something
that has all-atom force fields, as I personally believe
Hi Stephen,
Is it possible for you to post the link to the articles you read about
mitochondrial simulations and the 200 membrane lipids?
Thanks in advance
Esteban
On Thu, May 13, 2010 at 12:00 PM, lloyd riggs lloyd.ri...@gmx.ch wrote:
Dear All,
I recentlly started using Gromacs again. I
Hi Stephen,
I am particularly interested in lipid .rtp libraries hopefully for something
that has all-atom force fields, as I personally believe simulations should be
as real as possible, and also believe non-polar hydrogens still illicite some
force in the overall scheme of the molecular
Dear all
I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
tar -xvzf xmgr-4.1.2.tar.gz
cd xmgr-4.1.2
./configure
make
make install
But it gives error command xmgr not found.
Please help.
shahid Nayeem
--
gmx-users mailing listgmx-users@gromacs.org
Command is xmgrace and it needs to be in your $PATH.
On 13 May 2010 12:19, shahid nayeem msnay...@gmail.com wrote:
Dear all
I downloaded xmgr-4.1.2.tar.gz and tried to install by following commands.
tar -xvzf xmgr-4.1.2.tar.gz
cd xmgr-4.1.2
./configure
make
make install
But it gives
manjula kasinathan wrote:
hi all
i have done protein protein interaction and the complex structure
was taken for MD simulation using Gromacs.while performing mdrun step
for position restrain i got error. i have carried out mdrun for 1ps and
the command given for mdrun
and
John Shultz wrote:
I am trying to rerun a simulation using this command
mdrun -rerun -v -deffnm md
I think I must have made a mistake when I prepared the original mdp
file because I get this message
Number of atoms in trajectory (3883) does not match the run input file (37770)
I have these
Thank you Justin, is there a way I can choose both Protein LIG? It has
the following options for me
Reading toplogy and shit from md.tpr
Reading file md.tpr, VERSION 4.0.5 (single precision)
5 steps (100 ps) remaining from first run.
Opening library file
John Shultz wrote:
Thank you Justin, is there a way I can choose both Protein LIG? It has
the following options for me
You need to make a custom group that merges these two.
-Justin
Reading toplogy and shit from md.tpr
Reading file md.tpr, VERSION 4.0.5 (single precision)
5 steps
I'm trying to energy minimise a protein structure. In one area of the
structure there are some salt bridges and when I do an energy
minimisation without any restraints these are disrupted, which is
something I want to avoid. To that end, I've tried restraining the
residues that are
Anna Duncan wrote:
I'm trying to energy minimise a protein structure. In one area of the
structure there are some salt bridges and when I do an energy
minimisation without any restraints these are disrupted, which is
something I want to avoid. To that end, I've tried restraining the
Why don't you simply define a extra bond between your two CYS side
chains beads?
On May 13, 2010, at 3:31 PM, Anna Duncan wrote:
I'm trying to energy minimise a protein structure. In one area of
the structure there are some salt bridges and when I do an energy
minimisation without
On May 13, 2010, at 3:58 PM, XAvier Periole wrote:
Why don't you simply define a extra bond between your two CYS side
chains beads?
Sorry, I red to quick ...
On May 13, 2010, at 3:31 PM, Anna Duncan wrote:
I'm trying to energy minimise a protein structure. In one area of
the
Hi there,
From what I've read and known, here in the list as well, one of the main
reasons why Gromacs run in single precision is because it has LINCS, besides
SHAKE, which I believe requires double precision for accuracy.
I am drawing such conclusion (that can be wrong) partially based on
Thanks for that. It would have taken me ages to spot the quotation
marks error...
Everything working fine now, of course...
On 13 May 2010, at 14:58, gmx-users-requ...@gromacs.org wrote:
Re: Use of restraints gives segmentation fault
--
gmx-users mailing listgmx-users@gromacs.org
Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
I have defined the residue name of solute (its glucose, one glucose
molecule) and solvent (its cations of ionic liquids, 128 cations) by group
numbers.
During the g_spatial calculation can I select this group
Nilesh Dhumal wrote:
Hello,
I am trying to calculate spatial distribution function (SDF) for my system.
I have defined the residue name of solute (its glucose, one glucose
molecule) and solvent (its cations of ionic liquids, 128 cations) by group
numbers.
During the g_spatial calculation can I
Hi!
We have a problem with a protein-ligand-protein simulation. It is a somewhat
large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
that requires a larger box for proper simulation.
We used exclusions (especifically for the problematic atoms) and restrictions
(tested
I think that I finally managed to get gromacs installed correctly. When I
type luck in the command line I get a random phrase. When I try to run
demo I get the following error messages:
dyld: Library not loaded: libmkl_intel_lp64.dylib
Referenced from: /Users/emily/gromacsfolder/bin/pdb2gmx
Hello,
I intend to generate a stack of molecules with the command line:
genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro
Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7 molecules
per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189 molecuels.
What I get from the
Dear all,
There was a similar thread in the archives, but I could not find the
solution to my problem from the only reply (nor in the manual).
I've been trying to add 3 h2po4 ions to my system, as these appear to
be tightly bound to the protein I want to use in my calculations.
I got
On 5/13/10 8:31 PM, Tiago Barros wrote:
Dear all,
There was a similar thread in the archives, but I could not find the
solution to my problem from the only reply (nor in the manual).
I've been trying to add 3 h2po4 ions to my system, as these appear to
be tightly bound to the protein I want
Moeed wrote:
Hello,
I intend to generate a stack of molecules with the command line:
genconf -f Hexane.gro -nbox 8 6 4 -o Hexane-STACK.gro
Hexane.gro has box size of 3*3*3 nm3 and I need to have about 7
molecules per nm^3. So I multiplied 7 by 27 (box size) to get (7*27=)189
molecuels.
Giovana Bergamini wrote:
Hi!
We have a problem with a protein-ligand-protein simulation. It is a somewhat
large system (approx. 360 amino acid residues with approx. 70 monosaccharides),
that requires a larger box for proper simulation.
We used exclusions (especifically for the problematic
Hi,
I am trying to calculate the relative free energy differences of
conformations of a peptide as a function of end-to-end distance (linear
distance between N-terminal nitrogen atom to C-terminal carbon atom).
According to the manual pull code should not be used because the
Emily Curtis wrote:
I think that I finally managed to get gromacs installed correctly. When
I type luck in the command line I get a random phrase. When I try to
run demo I get the following error messages:
dyld: Library not loaded: libmkl_intel_lp64.dylib
Referenced from:
- Original Message -
From: Emily Curtis emilymariecur...@gmail.com
Date: Friday, May 14, 2010 5:12
Subject: [gmx-users] luck works but demo fails
To: gmx-users@gromacs.org
I think that I finally managed to get gromacs installed correctly. When I
type luck in the command line I get a
I need to do water channel simulations... I have two gro files with me...one
for wall atoms and one for water atoms...assuming the co-ordinates of atoms
are appropriate, I just need to rename the indices of each atom
appropriately and append one file to anotherI plan to do it by
hand...but it
Sikandar Mashayak wrote:
I need to do water channel simulations... I have two gro files with
me...one for wall atoms and one for water atoms...assuming the
co-ordinates of atoms are appropriate, I just need to rename the indices
of each atom appropriately and append one file to anotherI
Hi
I am simulating a system consisting of a protein embedded in membrane,
solvated with water using the Martini forcefield. I have set up a free
energy perturbation simulation where a subset of the protein particles are
being converted from their original particle type (state A, lambda =0) to a
yeah I know its simple, but only concern I have is that, the index of
atom/residue in two files may not be in agreement, so I have to change/shift
index of atoms in one of the file.
but anyway I guess I will have to do it manually
thanks
sikandar
On Thu, May 13, 2010 at 10:02 PM, Justin A.
Sikandar Mashayak wrote:
yeah I know its simple, but only concern I have is that, the index of
atom/residue in two files may not be in agreement, so I have to
change/shift index of atoms in one of the file.
but anyway I guess I will have to do it manually
That part can be done with
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