[gmx-users] Simulate only one unit of the virus capsid while fixing its surrounding units

[ZHANG Cheng]

It is a challenge to simulate the entire virus as it is too big and I do not have such computational resources. So I was thinking to only simulate one coat protein and its surrounding neighbours, but keep the neighbours relatively fixed.


Can I ask


1) Is this a sensible idea to proceed?


2) To fix the neighbours, should I use "constraints" or "restraints"?


3) At which step should I start to introduce the fixation?


4) If possible, is there a tutorial for this? I feel the information here is still not straightforward to follow
http://www.gromacs.org/Documentation/How-tos/Position_Restraints


Thank you!


Yours sincerely
Cheng