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.* 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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