[gmx-users] gmx covar: Segmentation fault

> Dear All, > > Anyone has experience with the covariance analysis program from gromacs? I > can’t get rid of the segmentation fault. I run the following: > > gmx covar -f md.xtc -s md.tpr -v eigenvec.trr -n sys.ndx > > And this is the output: > > Choose a group for the least squares fit > Gr

Re: [gmx-users] gmx covar: Segmentation fault

Why is it reading one frame more than the last frame number?… Could that be a bug? > On 20 Apr 2016, at 16:51, Oliwia Maria Szklarczyk wrote: > > Dear All, > > Anyone has experience with the covariance analysis program from gromacs? I > can’t get rid of the segmentatio

[gmx-users] gmx covar: Segmentation fault

Dear All, Anyone has experience with the covariance analysis program from gromacs? I can’t get rid of the segmentation fault. I run the following: gmx covar -f md.xtc -s md.tpr -v eigenvec.trr -n sys.ndx And this is the output: Choose a group for the least squares fit Group 0 ( Lig

[gmx-users] alchemical thermodynamic integration in gromacs 5.0 - bonded lambdas

Dear All, I would like to run a free energy calculation using thermodynamic integration. The alchemical process I am simulating is a mutation of a alanine to a leucine in a protein. So I am creating new atoms and interactions. I changed the topology file such that new types of atoms, bonds, ang

[gmx-users] refining a TI calculation - additional lambda points

Dear All, I was wondering if you have tips on how to easily create additional lambda points in a thermodynamic integration calculation in gromacs 5. I have 21 lambda points already simulated, from L_0 to L_20, and now I need six more lambda-points between L_16 and L_19. Cheers, oliwia -- Gro