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

[Mark Abraham]

Hi,

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:
>

http://www.gromacs.org/Documentation/Terminology/Constraints_and_Restraints

Mark


> 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>
>
>
> --
> 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-request at gromacs.org.
>