> Thank you Thomas and Justin for your valuable suggestion. > Thomas and Justin, my Query is as follow...... > > In step six ..We are doing NPT equilibration followed by production run.... > The mdp files for both is same(Except the time of run and saving of > output).... > So why the two mdp are same????? Why we not restrain total protein for > NPT equilibration (-DPOSRES) > and then only POSRES_B (Position restrain on B chain, remove position > restrain from other chain) > for production run..(these we follow generally)??? > > The main reason of confusion to me is the same mdp file in > Equilibration(npt_umbrella.mdp ) > and production run (md_umbrella.mdp). So what is the difference between > the NPT equilibration > and production run.??? > > As per Thomas explanation I interpret the following Answer to my Queries.. > Please tell me these are right or wrong .... > > > * > So if you want to calculate some equilibrium property of a protein in > water you do > first a preperation simulation to equilibrate the system (NVE, NVT or NPT > - depending > for what ensemble you want the property).Normally during this you put > position restraints > to the protein backbone, so that the protein structure does not gets > disturbed during the part where you equilibrate the water. but if your > protein is fairly stable / rigid, you don't need these > restraints.....(Thomas Explanation) > * > my Interpretation is as follow .... >
> So as the protein is stable thats why we are not using the position > restrained in NPT.. > That is the reason the npt_umbrella.mdp and md_umbrella.mdp looks same. > > > > Please accept my apology if I interpret any wrong and if unable to explain > you my query.. > > Thanks to Justin and Thomas for there valuable guidance.... > > I will be a very greatfull to you if you help me to solve my simple > query.. > > > Thank you in advance... > > > With Best Wishes, > Rama David. > > > > >
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