Parul Goel

7 Questions 1 Answers 0 Followers

Questions related from Parul Goel

How to interpert PMF graph in umbrella sampling ?

Hi, all I am new to umbrella sampling, I have the done simulation of 2 gold nanoparticles coated with ligand and interaction with 2 different groups: Case 1: with atp Case 2: water But my PMF...

13 October 2023 4,629 0 View

HOW TO SOLVE FOLLOWING ERROR IN GROMACS :Check for bad contacts and/or reduce the timestep if appropriate?

I am facing this error while nvt simulation constantly i am done trying adding -dflexible flag using steep integrator during em also and nvt,mdp also,still error persists how to resolve it , i am...

29 March 2023 3,579 0 View

Energy minimization has stopped ?

Using 1 MPI thread Using 8 OpenMP threads WARNING: Using the slow plain C kernels. This should not happen during routine usage on supported platforms. Back Off! I just backed up em.trr to...

28 February 2023 1,693 1 View

How to resolve LINCS warning error in gromacs during Equilibration(NVT) mdrun?

gmx mdrun -deffnm nvt Back Off! I just backed up nvt.log to ./#nvt.log.1# Compiled SIMD: SSE4.1, but for this host/run AVX2_256 might be better (see log). Reading file nvt.tpr, VERSION...

16 December 2022 8,646 1 View

I am trying to do the pulling of my non-protein system in the umbrella sampling but i am getting this error & even if I put ‘pull-group1-pbcatom' = 0?

Input command : gmx grompp -f md_pull.mdp -c npt.gro -p topol.top -r npt.gro -n index_ligand_au.ndx -t npt.cpt -o pull.tpr -maxwarn 3 :-) GROMACS - gmx grompp,...

30 November 2022 7,671 1 View

How can i calculate center of mass for a molecule ?

i am trying to do umbrella sampling of 2 AU molecules but whenever I am trying to run the md_pull.mdp file it giving an error : ERROR 1 [file md_pull.mdp]: When the maximum distance from a pull...

23 November 2022 1,294 1 View

How can I calculate center of mass for a molecule(AU)?

How can I calculate center of mass for a molecule(AU)? Hello every body I want to calculate the center of mass for a molecule I want to know which atom the center of mass hold on. pleas give me a...

23 November 2022 5,756 5 View