[gmx-developers] Calling do_steep from within do_md integrator

[David van der Spoel]

On 2015-02-07 17:44, Andrew AbiMansour wrote:
> Hi Mark,
>
> Thank you for the reply. I decided to just test my own simple SD
> integrator. After calling do_force() I update the positions. Example:
>
> int i = 0, dim = 3;
> real sd_step_size = 0.01;
>
>     for(i = 0; i < mdatoms->nr; i++)
>                       for(d = 0; d < dim; d++) {
>                                 state->x[i][d] += sd_step_size * f[i][d];
>
>
> The code *works* , but the output doesnt make much sense. When I print
> the force (f[i][d]), I get a lot of zeros. Am I doing this right? I'm
> afraid I might not be accessing the forces (stored locally on each
> processor) correctly. Any suggestions?

It would be helpful to know what you are trying to achieve. Maybe the 
functionality can be found in the routine relax_shells_fc already?

>
> Thanks!
>
>
> *Andrew Abi-Mansour*
>
> On Sat, Feb 7, 2015 at 6:54 AM, Mark Abraham <mark.j.abraham at gmail.com
> <mailto:mark.j.abraham at gmail.com>> wrote:
>
>     Hi,
>
>     Probably you are over- or under-managing periodic boundaries and/or
>     domain decomposition. I would think you should refactor out of
>     do_steep exactly the part you need, since it's not designed to be a
>     callable utility routine. For example, you probably don't want it to
>     ever call em_dd_partition_system()...
>
>     Mark
>
>     On Sat, Feb 7, 2015 at 7:15 AM, Andrew AbiMansour
>     <anabiman at umail.iu.edu <mailto:anabiman at umail.iu.edu>> wrote:
>
>         Hi,
>
>         I would like to call the integrator function do_steep() from
>         within do_md(). I modified some constraints parameters in
>         t_inputrec before passing all the arguments supplied to do_md()
>         by the user to do_steep(). This simple approach, however, does
>         not work and GROMACS crashes complaining about a charge group
>         moving too far. The coordinates seem to change by several nano
>         meters over a single SD step. What is this happening? and Do you
>         have any suggestions on how to implement this right?
>
>         Thanks
>
>         *Andrew Abi-Mansour*
>
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-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205.
spoel at xray.bmc.uu.se    http://folding.bmc.uu.se