[gmx-users] Break ? => Position restrained MD
Mark.Abraham at anu.edu.au
Thu Dec 31 03:42:27 CET 2009
Chih-Ying Lin wrote:
> In the position restrain MD, only solvent molecules and hydrogen atoms
> are allowed to move...
.... appreciably under normal conditions. However if you have a medium
restraining force and a ridiculously large LJ force, guess who wins?
> I checked the .out file.
> The max is happened on the atoms inside protein.
Probably because they were overlapping with some other atoms initially.
Try setting up a simpler simulation system until you work out how to get
things right. Definitely record each step as you do it (e.g. copy and
paste your terminal history after using "history") so you know what
you're doing where.
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