Davood Zaeifi

4 Questions 20 Answers 0 Followers

Questions related from Davood Zaeifi

How can I give an octahedron box in gromacs, prefered dimension ?

Hi all I have almost use the following command to give dimension to membrane, which is octahedron ! gmx editconf -f *.gro -o *-box.gro -bt octahedron -d 1.0 -c Now I `m trying to give a right...

06 June 2016 8,358 2 View

Topol.top in gromacs ?

If you separately create topology for your ligand and your lipid but via same name, the second topology has been added to previous topology file or create absolutely different topology file but...

05 May 2016 4,836 3 View

Applying Charmm36 forcefield in gromacs or accelrys ?

I tried to apply charmm36 forcefield to my mixed lipid bilayer in two software different software (gromacs, accelrys). But in gromacs, error coming up with: POPE1 could not be recognized as...

05 May 2016 9,598 3 View

How can I modify the InflateGRO script for packing my bilayer lipid with 2 type or mixed residue ?

I have made a popg:pope bilayer lipid via charmm gui online for molecular dynamic purpose. But i could not pack my lipid via inflate script because it works only for ine type lipid.

04 April 2016 1,575 9 View