[gmx-users] help - pr

lalitha selvam hayagrivar at hotmail.com
Fri May 19 11:05:39 CEST 2006

Dear sir,

1.i'm trying to dock my protein with the ligand.for the ligands i want to do 
energy minimization.shall i do em.mdp step alone to get the energy minimized 
ligand structure for my docking studies.can i make use of that structure 
which got out of using gromacs software with the energy minimization step 
alone..........or else i've to continue full dynamics step........

2.one more doubt is how to fix up the time for equilibration step.i set 
500ps for my protein to do pr.........but i do not know whether it is 
correct or not.the thing is i want to know how much time the PR step sh'd be 
carried out...if it depends upon our protein length means also - how?

thank u in advance.


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