On 01/27/11, bharat gupta bharat.85.m...@gmail.com wrote:
I actually don't understand exactly what u are asking .. since I am not an
expert with gromacs..
Please leave the old context for the discussion in future emails. Only you are
paying so much attention to your work that you can be
Mark Abraham wrote:
On 01/27/11, *bharat gupta * bharat.85.m...@gmail.com wrote:
I actually don't understand exactly what u are asking .. since I am
not an expert with gromacs..
Please leave the old context for the discussion in future emails. Only
you are paying so much attention to
I generated the secondary structure profile of structure retrieved from the
last frame of the simulation ... In that profile those amino acids that are
shown as loops in VMD doesnot have any secondary structure assignment ... it
means that during simulation the structure got changed some how ...
bharat gupta wrote:
I generated the secondary structure profile of structure retrieved from
the last frame of the simulation ... In that profile those amino acids
that are shown as loops in VMD doesnot have any secondary structure
assignment ... it means that during simulation the structure
I used the same .mdp files that are given in the lysozyme tutorial .. Since
I was knowing what all parameters to change .. but after energy minimization
and equilibration steps , the graphs that I got were fine ... even the rmsd
graph of the final structure is also fine .. I have attached the
On 27/01/2011 11:11 PM, bharat gupta wrote:
I used the same .mdp files that are given in the lysozyme tutorial ..
Since I was knowing what all parameters to change .. but after energy
minimization and equilibration steps , the graphs that I got were fine
... even the rmsd graph of the final
I don't think that there is any problem in the structure .. since I am
simulating the crystal structure taken from PDB ... and I have checked the
structure generated after pdb2gmx and solvation..
Since I am reapeating the simulation again I want to know and I am on energy
minimzation step I want
bharat gupta wrote:
I don't think that there is any problem in the structure .. since I am
simulating the crystal structure taken from PDB ... and I have checked
the structure generated after pdb2gmx and solvation..
Since I am reapeating the simulation again I want to know and I am on
I didn't gave any -c flag while md run .. and there is no confout.gro in
my folder .. I have attached the graph obtained after energy minimzation ..
I want to ask why the graph is not coming like the one shown in the tutorial
.. I guess I asked that same question earlier also ?? .. Here is
bharat gupta wrote:
I didn't gave any -c flag while md run .. and there is no confout.gro in
my folder .. I have attached the graph obtained after energy minimzation
I've never heard of such a thing. mdrun produces several files automatically:
traj.trr, ener.edr, md.log, and confout.gro.
Hi Bharat,
If you have used the -deffnm option then the output gro will be called
whatever name you used for the -deffnm option and not the default
confout.gro.
Tom
Justin A. Lemkul wrote:
bharat gupta wrote:
I didn't gave any -c flag while md run .. and there is no confout.gro in
my
On 01/27/11, bharat gupta bharat.85.m...@gmail.com wrote:
Hi,
I did a 3ns simulation of a 236 amino acid protein (GFP, a beta barrel
protein), after checking the trajectory it seems that from the first frame
itself almost half portion of the two beta strands (159-171, 174-187) of GFP
I actually don't understand exactly what u are asking .. since I am not an
expert with gromacs..
I don't know when is was written .. Here are some lines from the log files
of simulation ...
Statistics over 151 steps using 31 frames
Energies (kJ/mol)
AngleProper Dih.
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