problem with MD

From: hamze rahimi (
Date: Tue Feb 15 2011 - 00:25:25 CST

Dear expert

I am teacher for computational biology.i worked with GROMACS for classic MD
but my student interest to NAMD you know in classic MD there are
three critical steps:
1- energy minimization
2- position-restrained
3- equilibration or molecular dynamic(MD) step

I read NAMD2.7 tutorial very carefully but i find only one configuration
file for energy minimization.therefore i start search in google, finally i
find a web site that contain related steps.

now i have some questions:
1- who do i can perform classic MD in NAMD?I need more information than namd
2- what is relation among these step in namd? in gromacs protocol is cascade
(step 1 output role as step 2 input and forward).i performed three steps
i can't find relation among these step because any step read ionized

thanks a lot for any help

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