Re: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)

, which can be considered as zero. do you know any reason of this, having only 4 (close to) zero eigenvalues ?? -- Hyuntae > Message: 3 > Date: Sun, 10 Mar 2013 23:10:05 +0100 > From: "lloyd riggs" > Subject: Re: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol >

Re: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)

; Betreff: [gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for > l-bfgs) > Dear, This is the same issue that I asked last time. I wonder (1) if I > setup the test wrong, (2) if NMA *can* have smaller than 6 eigenvalues even > though the conformation of a protein is in

[gmx-users] only 4 zero eigvals for NMA (with 10^-6 emtol for l-bfgs)

Dear, This is the same issue that I asked last time. I wonder (1) if I setup the test wrong, (2) if NMA *can* have smaller than 6 eigenvalues even though the conformation of a protein is in equilibrium in the enough degree, or (2) if it gromacs does not make it in equilibrium because of the lim

[gmx-users] only 4 zero eigvals for NMA

Dear, I am studying several protein fluctuation proteins using NMA (Normal Mode Analysis). In the mean time, I found out in many cases that NMA hessian matrix has about 3-4 zero eigenvalues even though having 6 zero eigenvalues are expected. I tried to reduce the tolerance level lesser than 10^-