An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Regarding RMSD analysis result
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I
followed
the similar condition for both
-Nachricht
Datum: Mon, 24 Sep 2012 04:32:33 -0700
Von: naga sundar naga25sun...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Regarding RMSD analysis result
Dear justin
Thanks for ur suggestions
It looks for me like the known pbc effect others already pointed to. If
you have just a protein-ligand complex (+ water and counterions of
course) it's relatively easy to manually (a piece of code would do it)
bring the ligand to the correct position in the frames showing an
abnormally high
Dear Felipe
Thanks for ur reply.
The system is a protein-protein complex. Like u r saying its due
to pbc problem then why any abnormality doesn't happened to the native
complex (Black line)?. As already suggest by justin i checked the pbc
conditions upto my knowledge
On 09/25/2012 10:08 AM, naga sundar wrote:
Dear Felipe
Thanks for ur reply.
The system is a protein-protein complex. Like u r saying its due
to pbc problem then why any abnormality doesn't happened to the native
complex (Black line)?.
Maybe because MD is stochastic
Hi,
Your RMSD graph is ok but is represented wrong due to pbc problem. Use
whole and nojump options of trjconv.
On Tue, Sep 25, 2012 at 2:15 PM, Felipe Pineda, PhD
luis.pinedadecas...@lnu.se wrote:
On 09/25/2012 10:08 AM, naga sundar wrote:
Dear Felipe
Thanks for ur
Hi,
trjconv -s top.tpr -f traj.xtc -o traj-nojump.xtc -pbc nojump
I hope it helps
2012/9/25 Archana Sonawani ask.arch...@gmail.com
Hi,
Your RMSD graph is ok but is represented wrong due to pbc problem. Use
whole and nojump options of trjconv.
On Tue, Sep 25, 2012 at 2:15 PM, Felipe
On 9/24/12 6:24 AM, naga sundar wrote:
Dear gromacs users
We performed MD simulation analysis for native and mutant
models of protein-protein complexes. From 20 ns simulation trajectory, we
generated RMSD graph for one native and three mutant complexes. For native
complex in the
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I followed
the similar condition for both native and mutant complexes. For native
complexes not any big deviation was observed. So its confirmed that nothing
wrong with
On 9/24/12 7:32 AM, naga sundar wrote:
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I followed
the similar condition for both native and mutant complexes. For native
complexes not any big deviation was observed. So
for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Regarding RMSD analysis result
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I followed
the similar condition for both native and mutant complexes
: [gmx-users] Regarding RMSD analysis result
Dear justin
Thanks for ur suggestions
While speaking about periodic conditions, I followed
the similar condition for both native and mutant complexes. For native
complexes not any big deviation was observed
have to centre it.
Stephan
Original-Nachricht
Datum: Mon, 24 Sep 2012 04:32:33 -0700
Von: naga sundar naga25sun...@gmail.com
An: Discussion list for GROMACS users gmx-users@gromacs.org
Betreff: Re: [gmx-users] Regarding RMSD analysis result
Dear justin
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