[gmx-users] removing degrees of freedome from different proteins at different timesteps of an md simulation

Filip Jagodzinski filip at cs.umass.edu
Fri Sep 12 06:03:07 CEST 2008

hi gmx-users,

i haven't been able to accomplish the following:

i have a system with n atoms, and i want to remove the degrees of freedom 
for some of the atoms during different moments of the simulation

for example, assume the primary sequence of my protein is a-b-c-d-e-f-g, 
and, for the first 50 picoseconds, i know that b, c and d move as a 
"group", and so i want to remove the degrees of freedome between b and c 
and between c and d, and have {bcd} move as one unit; then, at time 50-100 
picoseconds, atoms b, c and d no longer more as a group, but atoms d, e, f 
and g move as a group, so for the integration step from 50 to 100 
picoseoncds, i would want to remove the degrees of freedome between d and 
e, between e and f, and between f and g

this is similar to fixing all but the active site of a protein and only 
performing md on only the active site, but not quite the same

any suggestions?

thanks much!


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