[gmx-developers] Define an new group

[Rebecca Kleemann]

I want it more like the freeze groups, but moving. It should be used 
like a frozen layer stabilizing a thin layer of solids, but with a 
constant velocity.
It's partly working, but I wasn't able to make a good (reasonable fast) 
build and installation on our HPC system, so I want to switch to 
easybuild and patching a version which is supported (max. 2019.4). As 
the way groups are defined was changed between 2016.3 and 2019.6 I'm 
thinking about trying to use one of the already defined groups to avoid 
problems with that.



Am 10.04.20 um 23:30 schrieb Erik Lindahl:
> That does make sense, and was actually how I recall the 
> implementation, but sadly it's not reflected in the documentation. 
> That says quite explicitly all atoms in the group will experience 
> constant acceleration, not merely have an acceleration factor added.
>
> Cheers,
>
> Erik
>
> On Fri, Apr 10, 2020 at 11:01 PM Berk Hess <hess at kth.se 
> <mailto:hess at kth.se>> wrote:
>
>     Hi,
>
>     Acceleration groups will not work as those add an extra force to a
>     group and do not keep the total acceleration constant.
>
>     I think that using a pull coordinate with absolute reference and
>     of constraint type should work, then you need to set a velocity
>     using the free-energy coupling with lambda and setting a pull rate.
>
>     Otherwise you can indeed use one of the two user groups.
>
>     Cheers,
>
>     Berk
>
>     On 2020-04-10 13:01, Erik Lindahl wrote:
>>     Hi Rebecca,
>>
>>     I have to confess it was a _long_ time since I looked into these
>>     parts of the code, but you might be able to achieve this simply
>>     by defining a group, giving it the initial velocity you want, and
>>     then using the constant-acceleration functionality with the value
>>     0.0 (since zero constant acceleration means constant speed).
>>
>>     And if that fails, it should be possible to fix it without too
>>     much effort :-)
>>
>>     Otherwise, the idea of the user groups is exactly that you should
>>     be able to quickly implement a small routine where you do
>>     something to an arbitrary group without having to redefine the
>>     input mdp options, create a new (incompatible) TPR version, and
>>     also having to modify the enum lists.
>>
>>     Cheers,
>>
>>     Erik
>>
>>     On Fri, Apr 10, 2020 at 12:55 PM Rebecca Kleemann
>>     <rkleeman at students.uni-mainz.de
>>     <mailto:rkleeman at students.uni-mainz.de>> wrote:
>>
>>         Hi,
>>
>>         I want to add a group to set atoms to a constant velocity.
>>
>>             enum
>>             {
>>                 egcTC,    egcENER,   egcACC, egcFREEZE,
>>                 egcUser1, egcUser2,  egcVCM, egcCompressedX,
>>                 egcORFIT, egcQMMM,
>>                 egcNR
>>             };
>>
>>             const char *gtypes[egcNR+1] = {
>>                 "T-Coupling", "Energy Mon.", "Acceleration", "Freeze",
>>                 "User1", "User2", "VCM", "Compressed X", "Or. Res.
>>             Fit", "QMMM", nullptr
>>             };
>>
>>         Are "User1" and "User2" meant to be used like that and can
>>         they be renamed or should I add a new group and increase the
>>         number of groups?
>>
>>         Greetings,
>>
>>         Rebecca
>>
>>         -- 
>>         Gromacs Developers mailing list
>>
>>         * Please search the archive at
>>         http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-developers
>>         or send a mail to gmx-developers-request at gromacs.org
>>         <mailto:gmx-developers-request at gromacs.org>.
>>
>>
>>
>>     -- 
>>     Erik Lindahl <erik.lindahl at dbb.su.se <mailto:erik.lindahl at dbb.su.se>>
>>     Professor of Biophysics, Dept. Biochemistry & Biophysics,
>>     Stockholm University
>>     Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>>
>
>     -- 
>     Gromacs Developers mailing list
>
>     * Please search the archive at
>     http://www.gromacs.org/Support/Mailing_Lists/GMX-developers_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-developers
>     or send a mail to gmx-developers-request at gromacs.org
>     <mailto:gmx-developers-request at gromacs.org>.
>
>
>
> -- 
> Erik Lindahl <erik.lindahl at dbb.su.se <mailto:erik.lindahl at dbb.su.se>>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm 
> University
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20200410/4e09d1f1/attachment.html>