Chenlin Lu

3 Questions 9 Answers 0 Followers

Questions related from Chenlin Lu

Why charge parameter of cations like Cu2+, Zn2+ in GROMOS 54a7 force field in GROMACS equals to zero?

I am trying to modify the original GROMOS 54a7 force field files implemented in GROMACS to add parameters of some new cations. But when I checked the ffnonbonded.itp, I found that the charge...

17 December 2018 1,903 4 View

Why do I only get one curve in histo.xvg when doing umbrella sampling analysis with Gromacs?

I am working on umbrella sampling with Gromacs. The procedure is based on Justin's tutorial. When I ran gmx wham -it tpr-files.dat -if pullf-files.dat -o -hist -unit kCal doing analysis, I got a...

05 May 2018 3,705 4 View

What to do if some residues are missing in crystal structure (PDB) while doing MD simulation?

What should we do if some residues are missing in crystal structure (PDB) while doing MD simulation? Sometimes, some residues of the proteins show less electron density in crystal analysis and...

01 January 1970 378 8 View