[gmx-users] simulation in vaccum

2012-04-28 Thread swati patel
Hello Everyone, I am trying to pull ligand biotin out of the streptavidin protein.Following the tutorial Protein ligand complex by Justin ,i have done till energy minimization step skipping adding solvent and ion step,and skipping pressure and temperature equilibration.Now how to proceed further t

Re: [gmx-users] Simulation in vaccum

2006-11-21 Thread Mark Abraham
nur avneet wrote: Dear ALL when we simulate in vaccum, first we do steepest descent, then conj, then md in vac. I want to know that, Do we use periodic boundary conditions here.. That depends if you want an isolated system in vacuo, or a periodic system in vacuo. and also if we dont spec

[gmx-users] Simulation in vaccum

2006-11-21 Thread nur avneet
Dear ALL when we simulate in vaccum, first we do steepest descent, then conj, then md in vac. I want to know that, Do we use periodic boundary conditions here..and also if we dont specify anything about pbc in mdp file wht does gromacs take it as... Also please tell me, is their any parti