Rubha Shri Gurunathan

5 Questions 8 Answers 0 Followers

Questions related from Rubha Shri Gurunathan

Regarding REMD simulation run ?

Hi, I would like to setup a replica exchange MD simulation in gromacs using GPU. Where I am using below command then I got an error. kidly help me in rectifying this Command line: gmx_mpi...

25 December 2024 2,155 3 View

error while running "gmx_MMPBSA -O -i mmpbsa.in -cs gromacs.pdb -ct traj.xtc -ci index.ndx -cg 1 13 -cp gromacs.top -o FINAL_RESULTS_M?

I have received error while running mmpbsa command "gmx_MMPBSA -O -i mmpbsa.in -cs gromacs.pdb -ct traj.xtc -ci index.ndx -cg 1 13 -cp gromacs.top -o FINAL_RESULTS_MMPBSA.dat -eo...

13 August 2024 9,766 0 View

How to run gmx_mmpbsa in a protein-ligand complex with a two hetatoms, NDP and UNK as ligand??

What is the command line for the same? When I try to run i got following error.... gmx_MMPBSA -O -i mmpbsa.in -cs md_0_200_final.tpr -ct final_10ns.xtc -ci index.ndx -cg 1 13 14 -cp topol.top -o...

13 June 2024 3,822 1 View

To simulate for 1000 nanoseconds (ns) in your Gromacs .mdp file, what should be set the nsteps parameter ?

Kindly suggest me

12 June 2024 515 4 View

Atom P1 in residue NDP 193 was not found in rtp entry NDP with 75 atoms while sorting atoms?

While performing gromacs MD simulation after pdbtogmx command using charmm force-field, i have received "Atom P1 in residue NDP 193 was not found in rtp entry NDP with 75 atoms while sorting...

03 June 2024 9,705 8 View