Re: [gmx-users] Regarding RMSD analysis result

2012-09-27 Thread Tsjerk Wassenaar
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-25 Thread naga sundar
-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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-25 Thread Felipe Pineda, PhD
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-25 Thread naga sundar
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-25 Thread Felipe Pineda, PhD
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-25 Thread Archana Sonawani
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-25 Thread ahmet yıldırım
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-24 Thread Justin Lemkul
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-24 Thread naga sundar
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-24 Thread Justin Lemkul
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-24 Thread lloyd riggs
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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-24 Thread Tsjerk Wassenaar
: [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

Re: [gmx-users] Regarding RMSD analysis result

2012-09-24 Thread ahmet yıldırım
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