[gmx-users] A question about general MD procedure

[Dallas B. Warren]

Can't really help you directly (and since noone else has chipped in with
something thought I'd at least give you some direction), but with
majority of things like this two things you can do to get things going:
read papers (and this emailing list) dealing with "similar things" and
play with various combinations / procedures yourself.  First bit will
give you a starting point, second will give you insight into how your
own system behaves with the various procedures and guide you to
something which is "right" for it.
 
Also, understand what each of the steps or procedures are actually for.
If it isn't applicable to your system (since majority deal with proteins
and your nanotube is very different to that) then there is no need to do
that.
 
Don't have any real idea on your axial compression, but you will apply
it during the MD part, as that is typically the production part of it
all, where you get all the information you are looking for.  Most naive
way I can see you would apply the compression is by increasing the
pressure in one of the axes, along the nanotube.  However, suspect it
will simply rotate around in the box when that is done.  Also depends on
whether it is an infinite tube versus of finite length, what will
influence the ways in which you can cause the compression.
 
Hope that provides some help for you.
 
Catch ya,

Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at vcp.monash.edu.au
+61 3 9903 9524
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
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