[gmx-users] Enc: 1-4 ineractions in double precision

Hi justin; I'm grateful for your help, but unfortunately I didn't solve the problem. I made a change in my mdp file. This is my mdout.mdp: == ; ;File 'mdout.mdp' was generated ;By

Re: [gmx-users] Residue interaction energy

Dear Justin, Thank you for your reply... Just to check if I made any mistakes is the following procedure acceptable? 1) make NDX file with extra groups RES and Protein_Without_RES 2) add options to the MDP file: energygrps = RES Protein_Without_RES non-Protein unconstrained_start = yes

Re: [gmx-users] Enc: 1-4 ineractions in double precision

Jessé Nóbrega wrote: Hi justin; I'm grateful for your help, but unfortunately I didn't solve the problem. I made a change in my mdp file. This is my mdout.mdp: Have you done sufficient energy minimization? Your simulation is crashing at step 0, which usually indicates unresolved atomic

Re: [gmx-users] Residue interaction energy

abelius wrote: Dear Justin, Thank you for your reply... Just to check if I made any mistakes is the following procedure acceptable? 1) make NDX file with extra groups RES and Protein_Without_RES 2) add options to the MDP file: energygrps = RES Protein_Without_RES non-Protein unconstra

[gmx-users] multiple eigenvectors with -linfix and the application of eigenvalues

Hello, When utilizing more than one eigenvector in make_edi -linfix, are the eigenvector linearly combined with their eigenvalues as coefficients, or does this combination occur in the absence of eigenvalues? Thank you, Chris. -- gmx-users mailing listgmx-users@gromacs.org http://lists

[gmx-users] how to obtain corresponding conformation for each point in the 2-D projection

Dear users for gromacs: We know that observing the sampled conformations in the subspace spanned by the eigenvectors is a so-called two-dimensional projection(2D projection), in 2-D projection, each point represents a snapshot from the simulation, and the distribution shows the sampled region along