Amit Kumar

5 Questions 13 Answers 0 Followers

Questions related from Amit Kumar

Is it possible to regain the topol.top file from tpr file?

Dear Sir, I am using gromacs and have mistakenly deleted topol.top and topol_Protein_Chain_*.itp files after running the simulation. But I need those files for calculating Interaction Energy and...

29 June 2020 5,116 0 View

Can anyone tell me why gromacs 4.5.5 is not generating data (not showing any error)?

Hi Everyone, I am trying to run REMD in implicit solvent using gromacs 4.5.5, where I am not getting output or any data file except a log file containing only developers' information. So, I am...

28 February 2020 9,409 4 View

How can I calculate configurational entropy along the complete trajectory of gromacs?

gmx anaeig calculates configurational entropy of the system. But it does give only one value of entropy. Is there any option I can use for calculating entropy along the complete trajectory?

03 February 2020 1,449 8 View

Why I am getting this error while installing Gromacs4.5.5?

I was trying to install gromacs4.5.5. I have followed the tutorial http://www.gromacs.org/Documentation/Installation_Instructions_4.5.5 using fftw3.1 and automake, openmpi. When I was using...

03 January 2020 5,313 0 View

I am simulating a protein in Gromacs in implicit solvent. But I am getting few errors. I tried some changes but nothing happened. Can you help?

This is the input file for equilibration. title = NVT Equilibration ; Run parameters integrator = sd ; leap-frog integrator nsteps = 250000 ; 2 * 50000 = 100...

22 November 2019 7,234 7 View