Re: [gmx-users] Protein RMSD high

2013-06-27 Thread tarak karmakar
No, it's not at all significant in my problem as the loop is not part of the active site, way far at the two termini. I have plotted the RMSD in presence and absence of the loop. In absence of the loop rmsd is coming around 0.3 nm. Thanks Mark Tarak On Thu, Jun 27, 2013 at 2:37 PM, Mark Abraham

Re: [gmx-users] Protein RMSD high

2013-06-27 Thread Mark Abraham
Your call. Is that motion significant to what you are trying to report by your observation of the RMSD? Mark On Thu, Jun 27, 2013 at 9:03 AM, tarak karmakar wrote: > Dear All, > > While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 > nm. I carefully looked at the trajector

[gmx-users] Protein RMSD high

2013-06-27 Thread tarak karmakar
Dear All, While simulating a protein, I see the rmsd fluctuates around a mean of 0.6 nm. I carefully looked at the trajectory (VMD movie) and saw there are two flexible terminii fluctuating with a very high amplitude contributing to the high value of RMSD. Is it ok to report this problem with this