Re: [gmx-users] RMSD from the average structure

Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the C-X bond causes the average positions of the hydrogens to line up. Consider using g_cluster to find representative

Re: [gmx-users] RMSD from the average structure

Dear Sir, Thanks for the useful insight. On Fri, Apr 26, 2013 at 2:21 PM, Erik Marklund er...@xray.bmc.uu.se wrote: Average coordinates are problematic and not generally representative. Consider for instance the average coordinates of a methyl group connected to X. The rotation around the

Re: [gmx-users] RMSD from the average structure

Hi Bipin Singh, That indeed gives you the RMSD against the average. Do think about it a bit more: do you want the average of the whole structure, or should you account for a phase of relaxation? Cheers, Tsjerk On Wed, Apr 24, 2013 at 2:17 PM, Justin Lemkul jalem...@vt.edu wrote: On

Re: [gmx-users] RMSD from the average structure

Thanks for your reply. Actually I am interested to see how much structural deviation is occurring in a protein during the simulation from its average position of atoms rather than the initial position (crystal structure or starting structure). The motivation of doing this analysis is the fact that

[gmx-users] RMSD from the average structure

Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. -- *--- Thanks and Regards, Bipin

Re: [gmx-users] RMSD from the average structure

On 4/24/13 3:06 AM, bipin singh wrote: Hi all, Please let me know whether this is the right way to calculate RMSD from the average structure from a simulation: g_rmsf -f traj.xtc -s average.pdb -od rmsdev.xvg average.pdb: is the pdb file produced using -ox option of g_rmsf. You can