[gmx-users] How to restrain the center of gravity

[Hirayama, Kazunori]

Hello, this is the first post for me. My apology for any rudeness.

My molecule of interest is a protein of about 12kD.
When I elevated temperature from 400K to 500K with .mdp file according to a tutorial, it seems that the proteins are shaking or parallel shifting.

Is it necessary for us to restrain the center of gravity? If so, could you show us which parameter to modify in .mdp file.

My parameters relevant to restraint are shown below:
define               = -DPOSRES              ; position restrain the protein

constraint_algorithm = lincs                 ; holonomic constraints
constraints          = all-bonds             ; all bonds (even heavy atom-H bonds) constrained
lincs_iter           = 1                     ; accuracy of LINCS
lincs_order          = 4                     ; also related to accuracy

Thank you in advance.

Kazunori Hirayama,
Bioscience Research Labs. Drug Discovery Research
Astellas Pharma Inc.
Tel: +81-29-863-7058 E-mail: kazunori.hirayama at astellas.com<mailto:kazunori.hirayama at astellas.com>