*Dear users*
*I am evaluating interaction of a ligand with a protein named amyloid. I
want to use 5 molecules of ligand in my simulation. I run the following
commands:*
>> pdb2gmx -f bamyloid.pdb -o bamyloid.gro -p bamyloid.top -water spc
then modifying the "bamyloid.gro" and adding 5 mols of li
On 5/2/14, 1:37 AM, rama david wrote:
Dear Friends,
I did MD simulation of two peptide that show that they form antiparallel
beta sheet structure after 120 ns . i used gromacs 4.5.5 version.
presently I completed MD simulation of another peptide (
Different sequence). but
On 5/2/14, 3:19 AM, Hamid Irannejad wrote:
*Dear users*
*I am evaluating interaction of a ligand with a protein named amyloid. I
want to use 5 molecules of ligand in my simulation. I run the following
commands:*
pdb2gmx -f bamyloid.pdb -o bamyloid.gro -p bamyloid.top -water spc
then modify
Hi,
I would suggest caution. I had a DPPC bilayer interacting with organic
molecules (beta naphthol) which are supposed to alter the phase behaviour.
The initial simulations using group cutoffs didn't capture one region of
the experimental phase diagram, even with 200 ns of simulation (SLIPIDS +
GA
I forgot to mention that the earlier simulations were with version 4.5.4
On Fri, May 2, 2014 at 6:13 PM, rajat desikan wrote:
> Hi,
> I would suggest caution. I had a DPPC bilayer interacting with organic
> molecules (beta naphthol) which are supposed to alter the phase behaviour.
> The initial
Dear friends,
Thank you Justin and Rajat for your suggestions.
I think it is really better to do all the MD in latest version or in the
same version.
That will avoid the unnecessary falls and critics.
With best regards,
Rama david
On Fri, May 2, 2014 at 6:13 PM, rajat desikan wrote:
> I f
Hi GMX-Users,
I'm trying to use trjcat command to join very large trajectories:
trjcat -f md_0_1.part*.xtc -s md_0_1.tpr -o all.xtc
but I found this error while gmx was reading the frames:
Reading frame2000 time 351750.000-> frame 70350 time 351750.000 ps
-> frame 70430 time 352150
Could anyone guide me to analyze protein-protein interaction energy
in a MD trajectory?
I'm simulating a dimer and want to see the interaction energy
between the two monomers.
Is it the same way like specifying the two chains (say residues
1-100 and in the other monomer residue
Dear Andrea:
I can't access your script now that posts have been removed from nabble.
I have tried changing demux.pl line 70
from:
$tstep = $log_line[6];
to:
$tstep = 0.002 * $log_line[4];
where 0.002 is my timestep. Did you do this or something similar?
Thank you,
Ch
Turns out I had to also change the printf specification from %-20g to %-20.2f
on lines 33 and 44 (the only two places where %-20g appears).
Seems to be working well now, although %-20.2f is not guaranteed to work if
exchanges are more frequent than 10 fs.
Chris.
__
Does gmxcheck on all the *part.xtc files give you the time ranges you
expect? What is your simulation time step and output period?
Mark
On Fri, May 2, 2014 at 5:30 PM, Giuseppina La Sala <
giuseppina.lasa...@unibo.it> wrote:
> Hi GMX-Users,
>
> I'm trying to use trjcat command to join very larg
When you run gmxcheck on md_0_1.part0014.xtc and md_0_1.part0015.xtc
separately, what start and end times do you get for each of the two files?
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Giuseppina La
Sala
Sent: 02 May 2014 11:
On 5/2/14, 12:32 PM, tarak karmakar wrote:
Could anyone guide me to analyze protein-protein interaction energy
in a MD trajectory?
I'm simulating a dimer and want to see the interaction energy
between the two monomers.
Is it the same way like specifying the two chains (s
Yes, gmxcheck gives me the time range that I expect for all my part*.xtc. I'm
an pretty sure that the files are not corrupted.
Infact I run the same command in the cluster were I performed the simulation
(and not in my local machine as previously) and this time everything went well
without prob
/waves his magic wand... You were on a FAT32 file system with 2GB file size
limits and about 350ns reaches that?
Mark
On Fri, May 2, 2014 at 11:44 PM, Giuseppina La Sala <
giuseppina.lasa...@unibo.it> wrote:
> Yes, gmxcheck gives me the time range that I expect for all my part*.xtc.
> I'm an pr
Hello everybody,
Let's say that I have a torsion potential, calculated at an ab initio level
and I want to develop parameters for GROMACS.
1) As I understand, I have to develop a topology (used acpype for that)
2) Then I took the topology and found all the dihedrals that include my
torsion of inte
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