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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
