[gmx-developers] Define an new group

[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> 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> 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
>> --
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>
>
> --
> Erik Lindahl <erik.lindahl at dbb.su.se>
> Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
> University
> Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
>
>
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-- 
Erik Lindahl <erik.lindahl at dbb.su.se>
Professor of Biophysics, Dept. Biochemistry & Biophysics, Stockholm
University
Science for Life Laboratory, Box 1031, 17121 Solna, Sweden
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