Re: [gmx-users] PCA and FEL

Allright Sir Thank you very much for clearing the point. With Regards Suniba Sent from my iPhone > On 15-May-2016, at 12:14 pm, Tsjerk Wassenaar wrote: > > Hi Suniba, > > No, you will get the stability of configuration in the order parameters you > choose. But you don't

Re: [gmx-users] PCA and FEL

Hi Suniba, No, you will get the stability of configuration in the order parameters you choose. But you don't know how much conformational freedom you have at each point. Low RMSD will mean stable, but a fixed point at high RMSD does not. Also note that the Rg is sort of part of the RMSD, which

Re: [gmx-users] PCA and FEL

Thank you very much Sir. I get you. Is it good enough to probe the stability of complex by projecting any two variables with free energy? like RMSD and Rg? Sent from my iPhone > On 15-May-2016, at 10:51 am, Tsjerk Wassenaar wrote: > > Hi Suniba, > > No, with gmx anaeig

Re: [gmx-users] PCA and FEL

Hi Suniba, No, with gmx anaeig you can select -2d, which does a 2D projection onto the selected eigenvectors. Alternatively, you can combine any two projections onto eigenvectors, which you get using the option -proj. The quickest way to do that is something like: paste <(grep -v '^[@#]'