[gmx-users] How to restrain the center of gravity
mark.j.abraham at gmail.com
Wed Nov 11 15:12:43 CET 2015
On Tue, Nov 10, 2015 at 11:03 AM Hirayama, Kazunori <
kazunori.hirayama at astellas.com> wrote:
> 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.
Internal vibrations are normal. Diffusion is normal. Crossing periodic
boundaries is normal. What do you think is a problem?
Is it necessary for us to restrain the center of gravity?
That's a question whose answer depends on what you're trying to achieve.
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
> 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>
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