[gmx-users] cosine content and nonconverged trajectory

Dear users, The cosine content of the principal components is an effective indicator for predicting whether or not a trajectory has been convergent. A high cosine content typically indicates a nonconverged trajectory (Chapter 5: Normal Modes and Essential Dynamics Steven Hayward and Bert L. de

Re: [gmx-users] cosine content and nonconverged trajectory

On 11/2/12 8:17 AM, ahmet yıldırım wrote: Dear users, The cosine content of the principal components is an effective indicator for predicting whether or not a trajectory has been convergent. A high cosine content typically indicates a nonconverged trajectory (Chapter 5: Normal Modes and

Re: [gmx-users] Cosine content

Hey :) This is pretty incorrect... A high cosine content is an indicator of unidirectional motion in phase space. I've elaborated on that on this list some while ago. Regarding your case, this means that, even if the RMSD is stable starting from 5ns, the protein still experiences random

[gmx-users] Cosine content

Dear Gromacs users I have a question regarding cosine content. I have a 50 ns trajectory and looking at the RMSD plot, i set aside the first 5 ns as the time required for stabilization and subsequently carried out a essential dynamics for the backbone atoms post 5ns. But when i perform a

Re: [gmx-users] Cosine content

Hi Vijayan, cosine content should say how not-random are the movements observed in the configuration set you have analized. Regarding your case, this means that, even if the RMSD is stable starting from 5ns, the protein still experiences random motions. You should therefore consider as

[gmx-users] cosine content

Dear users, When are checking the cosine content of a PC, (Pls. Correct me if I am wrong) This is the command we use - g_analyze -f input-principle-component.xvg -cc outputcosine content.xvg and for first PC output says - Cosine content of set 1 with 0.5 periods: --- for nth PC also it says