Hi Justin,
thank you very much for your help!!
On 7/8/12 6:02 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
thank you for your answer.
Now I tried it with two different restraint .itp files. One for the
protein and one for the dummy atoms.
But still it doesn't work.
Both behaviours are possible. Check the -mol option.
Javier
El 08/07/12 18:30, Ivan Gladich escribió:
Dear all
I am running a simulation of water slab, i.e. a water system with two
air/vacuum interface, using a 5 site water model.
I am doing a simple test calculating the water diffusivity by
If you want to pull along a vector which connects to groups, the easiest
way is to run 'g_dist' over your starting *.gro file.
this measures the distance and the vector connecting both groups. From
GROMACS-4.0.x you don't need to normalise the vector. So you can
directly use this vector.
Hi Gromacs friends,
I am trying to reproduced the result of article ¨Antimicrobial
peptide in Action¨
Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q
As per article they used two conditions,
1. Stress free ( Lateral Tension = 0)
2. Stress condition ( Lateral tension =
Hi
To see folding events in your (very) long peptide in explicit solvent,
without doing long MD ( 100 ns), you will need to use more complex MD
approach such as REMD or metadynamics. REMD is implemented in gromacs, but
for the latter one, you can use plumed with GROMACS.
See for example
Dear All,
Please suggest me any paper/article that contains force field
parameters for Mn 2+ .
Thanks
--
Tarak Karmakar
Molecular Simulation Lab.
Chemistry and Physics of Materials Unit
Jawaharlal Nehru Centre for Advanced Scientific Research
Jakkur P. O.
Bangalore - 560 064
Karnataka, INDIA
On 7/9/12 12:02 AM, bharat gupta wrote:
Hi,
I have been trying to study folding of a peptide 24 residues long. I
did a simulation of 50 ns with explicit solvent, CHARMM FF, but I
was not able to find even a single folding event. Then I decided use
explicit solvent for simulation and I
I was performing simulations on urea unfolding of protein. I performed
one set of simulation for 50 ns with a velocity (set by gen_seed) and
it went fine.
Now when I am doing simulation using a different gen_seed from 10 to
20 ns many long bonds are formed. I could visualize them in vmd.
On 7/9/12 7:09 AM, siddhant jain wrote:
I was performing simulations on urea unfolding of protein. I performed
one set of simulation for 50 ns with a velocity (set by gen_seed) and
it went fine.
Now when I am doing simulation using a different gen_seed from 10 to
20 ns many long bonds are
Hi,
we published recently a paper where we determined the oplsaa parameters for
Mn2+;
have look to (supp mat):
http://onlinelibrary.wiley.com/doi/10.1002/anie.201202032/abstract
hope it helps
On 07/09/2012 12:21 PM, tarak karmakar wrote:
Dear All,
Please suggest me any paper/article that
Hi :)
I got the parameters of the first 3 residues of the peptide and when I got
0.008e for total charge of the first 2 residues ( formyl and valine). It is
expected to be zero.
Is the 0.008e acceptable? Or I look for an other way to get the correct
parameters and charges?
Hi everybody,
I want to do a md for a protein with a membrane around it.
I already minimised the energy of the protein.
Output of the minimization:
^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02,
atom= 1653
Stepsize too small, or no change in energy.
Converged to machine
When I run the md run again I get still the already mentioned error and
additionally this one:
Fatal error:
66 particles communicated to PME node 2 are more than 2/3 times the
cut-off out of the domain decomposition cell of their charge group in
dimension x.
This usually means that your system is
On 7/9/12 9:25 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi everybody,
I want to do a md for a protein with a membrane around it.
I already minimised the energy of the protein.
Output of the minimization:
^MStep= 812, Dmax= 1.4e-06 nm, Epot= -7.59283e+05 Fmax= 3.59781e+02,
Hi Justin,
okey then I will try it with this timestep.
No it is not my goal to do a NVE. I already had temperature coupling
options in my .mdp file but on the blowing up side was written you are
using inappropriate temperature coupling so I thought that that might be
the reason and deleted it
On 7/9/12 9:40 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
Hi Justin,
okey then I will try it with this timestep.
No it is not my goal to do a NVE. I already had temperature coupling
options in my .mdp file but on the blowing up side was written you are
using inappropriate
With the mentioned below options I get the following error:
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
But it
Dear all,
I have done protein-ligand dynamics.I got the final gro file.When
converted to PDB, i observed that my active site has ligand but two
chains of teh protein got separated. What might be the reason for
this?should i consider this as an error in my simulation???kindly help
me in this
On 7/9/12 9:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
With the mentioned below options I get the following error:
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
On 7/9/12 9:48 AM, Ramya LN wrote:
Dear all,
I have done protein-ligand dynamics.I got the final gro file.When
converted to PDB, i observed that my active site has ligand but two
chains of teh protein got separated. What might be the reason for
this?should i consider this as an error in my
Thanks a lot Justin
On Mon, Jul 9, 2012 at 7:21 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/9/12 9:48 AM, Ramya LN wrote:
Dear all,
I have done protein-ligand dynamics.I got the final gro file.When
converted to PDB, i observed that my active site has ligand but two
chains of teh
I already decrease it to 0.002 as you said and then there comes this error
I wrote to you.
Now It try it with 0.001. It is still running.
Thank you for your answer.
Eva
On 7/9/12 9:46 AM, reising...@rostlab.informatik.tu-muenchen.de wrote:
With the mentioned below options I get the following
Hello, I'm trying to solvate an OPLSAA methanol molecule in
polarizable water shell.
Initially I generated a box of pure water using the TIP5P box
available in gromacs 4.5.
I simulated pure water and I got all the bulk properties in agreement
with published results for SW water.
In sequence, I
Hi Gromacs friends,
I am very novice to the lipid simulation study..
My problem may be very simple, But very imp to me to know it.
I am trying to reproduced the result of article ¨Antimicrobial
peptide in Action¨
Published in JACS, 2006,128, 12156-12161, doi no = 10.1021/ja062927q
As per
Oh !! nice work
Thanks a lot for the quick reply. But I'm very sorry to inform you
that whichever table [supplementary table S4] you are specifying in
the supporting info, I couldn't find anywhere. So, may be I'm finding
my way in wrong track. Can you please provide me the link and / the
table
On 7/9/12 1:21 PM, tarak karmakar wrote:
Oh !! nice work
Thanks a lot for the quick reply. But I'm very sorry to inform you
that whichever table [supplementary table S4] you are specifying in
the supporting info, I couldn't find anywhere. So, may be I'm finding
my way in wrong track. Can you
sorry it's my mistake .
thanks a lot for the reply.
On Mon, Jul 9, 2012 at 10:55 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 7/9/12 1:21 PM, tarak karmakar wrote:
Oh !! nice work
Thanks a lot for the quick reply. But I'm very sorry to inform you
that whichever table
Dear gmx friends,
Is there the best water model for each force fields? Which options are supposed
to be noticed in applying the best water model.
I need to tell you that I apply C36 in my simulations.
Thanks in advance.
Sincerely,
Shima
--
gmx-users mailing listgmx-users@gromacs.org
For CHARMM the typical water model is TIP3P, although I tend to use TIPS3P
since it's been reported on the mailing list to give better interactions with
bilayers. (Also easier to pass by picky reviewers at the expense of ns/day,
obviously).
The following thread may be helpful too:
Hello,
I followed below steps using VMD and GROMACS but something went wrong in
using GROMACS which I am not able to figure out. Appreciate your help.
1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2
2. VMD: within 5 of nucleic
$sel writepdb initialfile_updated.pdb
On 7/9/12 4:07 PM, SatyaK wrote:
Hello,
I followed below steps using VMD and GROMACS but something went wrong in
using GROMACS which I am not able to figure out. Appreciate your help.
1. editconf -f initialfile.pdb -o initialfile.gro -d 0.2
2. VMD: within 5 of nucleic
I'm trying to run a kinase (what means that I had ATP - large charged
group) energy minimization and then MD.
But when I put my protein together with its ligands I gotcha the
follow error message:
There is no domain decomposition for 6 nodes that is compatible with
the given box and a minimum
On 7/9/12 4:23 PM, Thales Kronenberger wrote:
I'm trying to run a kinase (what means that I had ATP - large charged
group) energy minimization and then MD.
But when I put my protein together with its ligands I gotcha the
follow error message:
There is no domain decomposition for 6 nodes that
On 7/9/12 4:25 PM, Justin A. Lemkul wrote:
On 7/9/12 4:23 PM, Thales Kronenberger wrote:
I'm trying to run a kinase (what means that I had ATP - large charged
group) energy minimization and then MD.
But when I put my protein together with its ligands I gotcha the
follow error message:
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