Doing position-restrained simulation is useful to equilibrate solvent and ions.
If you would like to study the dynamics of the peptide, PRMD doesn't help. PRMD
is usually performed before production run for a duration from several hundred
ps to 1ns.
Regards,
Yang Ye
----- Original Message ----
From: sarbani chattopadhyay <[EMAIL PROTECTED]>
To: gmx-users@gromacs.org
Sent: Tuesday, October 23, 2007 1:35:14 PM
Subject: [gmx-users] Position restricted md
Hi,
I am new to the field of MD.I want to know what is the effectivity of
position restricted MD
ie. where is the advantage of doing Position restricted MD.I have a small
peptide of 3
reidues.Is it necessary to do a Position restricted MD. What difference will it
make?
I may sound very unintelligent but any
suggestions are welcome.
THANKS in advance.
Sarbani
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