[gmx-users] Mass Weighted Covariance matrix

Hello I am trying to calculate mass weighted covariance matrix using a Gromacs Topology file and a trajectory file . The trajectory has only protein coordinates. I am using "gmx_mpi covar" function for the same. I am using following format from the documentation: gmx_mpi covar -f -s -ascii

[gmx-users] WHAM with Pull coordinate angle-axis

Dear GROMACS users, I used the new Pull Geometry angle-axis to define the angle between a peptide (with two c-alpha atoms) and the z-axis as pull coordinate. I have generated a pull trajectory where this angle changes over time from about 80 degree to 0 degree approximately, over the total time

Re: [gmx-users] KALP-15 tutorial

Actually, I thought that I made an error by minimizing system.gro instead of system_inflated.gro. So, I ran energy minimization for system_inflated.gro by renaming tutorial's minim.mdp as em.mdp- gmx grompp -f em.mdp -c system_inflated.gro -p topol.top -o inflated_em1.tpr But, I am again getting

Re: [gmx-users] gmx: malloc(): memory corruption

I have just reinstalled and run with gromacs 5.1.2, It's okey although performance is smaller when comparing to gromacs 2016.1 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] KALP-15 tutorial

After using this step- *perl inflategro.pl system.gro 4 DPPC 14 system_inflated.gro 5 area.dat* Reading. Scaling lipids There are 128 lipids... with 50 atoms per lipid.. Determining upper and lower leaflet... 64 lipids in the upper... 64 lipids in the lower leaflet

[gmx-users] gmx: malloc(): memory corruption

Dear GMX user, I have just installed *gromacs 2016.1* on my machine and run mdrun with these option: - title = 50AT DNA MD simulation ; Run parameters integrator = md