Desh Deepak Yadav

3 Questions 6 Answers 0 Followers

Questions related from Desh Deepak Yadav

How can one incorporate protons(H atoms) after obtaining polymer structure file(PDB) from CHARMM-GUI ?

We know charmm-gui polymer builder mostly builds neutral polymers. But what if someone wants a positively or negatively charged polymer, how can we introduce such atoms ? I know the H++ server...

26 October 2022 732 3 View

How to fix this atomic jumps in VMD ?

Hi there, I am simulating an all-atom system containing a polymer molecule in water. But after seeing the trajectories, many of the atoms seems to be shifted during the whole trajectory. I have...

17 October 2022 6,534 2 View

How is the nomenclature of different Force Fields being done ?

I want to understand the idea behind suffix numbers or letters of Force Fields such as AMBER94,AMBER96,AMBER99,AMBER99SB,AMBER99SB-ILDN,AMBER03 ,AMBERGS ,CHARMM22, CHARMM27, CHARMM36, GROMOS...

19 August 2022 7,880 3 View