Susheel Pangeni

4 Questions 6 Answers 0 Followers

Questions related from Susheel Pangeni

How do we fix badly or non equilibrated configurations in gromacs?

Program: gmx mdrun, version 2019.1 Source file: src/gromacs/mdlib/sim_util.cpp (line 752) MPI rank: 3 (out of 4) Fatal error: Step 700: The total potential energy is nan, which is not finite. The...

11 November 2019 7,345 2 View

How can we fix the Gromacs simulation for curvature of lipid system with hydrophobic wall?

To address this, we have included following code in the .mdp file of minimization, equilibration and production of gromacs files. define = -DDUMY_POS_RES We tried three...

10 October 2019 7,335 1 View

How can we utilize position restraint option in gromacs to run curvature based lipid simulation for some microseconds?

For lipid membrane curvature system

10 October 2019 8,441 3 View

How can we improve minimization in Gromacs for lipid membrane system?

I have concern about the comment of gromacs output that energy minimization reached the maximum number of steps before the forces reached the requested precision. Here's the output of...

10 October 2019 2,550 7 View