[gmx-users] MD exit condition

[Eric Smoll]

Hello Gromacs users,

In response to a question on setting a group-group distance as an MD exit
condition, Mark Abraham suggested that it might be possible to use a
table-specified bond that would terminate a simulation by generating an
infinite force and crashing mdrun.

I am interested in revisiting this idea with a slightly more complex exit
condition. How would I define a simulation that will crash when the
z-component of a fictious bond between two groups exceeds a certain value
in a specific cartesian direction (e.g., the z-component)? Is this
impossible in GROMACS?

Best,
Eric

On Thu, Aug 28, 2014 at 6:58 AM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> On Thu, Aug 28, 2014 at 3:32 PM, Eric Smoll <ericsmoll at gmail.com> wrote:
>
> > Hello Gromacs users,
> >
> > I am using Gromacs 4.6.5
> >
> > Is there a way to set an exit condition during a simulation? I am
> > interested in terminating dynamics when two groups are separated by a
> > certain distance.
> >
>
> No. People want this, but it's never been a priority for someone with the
> knowledge to implement it. Creative use of a bond with a "malware" user
> table could produce infinite forces that will get mdrun to blow up shortly
> after the condition is reached, but I can't honestly recommend that! :-D
>
> One reasonable approach might be to use the pull code to achieve the
> distance in a controlled way.
>
> If it is not possible to set an exit condition, I suspect I can post
> > process the trajectory with trjconv using the -exec flag and/or the
> -trunc
> > flag:
> >
> > 1.) The manual states that the -exec flag will "Execute a command for
> every
> > output frame with the frame number as argument." What kinds of commands I
> > can pass to this flag?
> >
>
> Intended for use with -sep or -split. Command gets passed the number of the
> file most recently written, and then has to go do its own file parsing. I
> would rather use g_dist or such.
>
> 2.) If the "-exec" is not useful, I plan to analyse the the output of
> > g_dist to find the the time "t" when two groups exceed my distance
> > criterion and run "trjconv -trunc t" to crop the trajectory
> appropriately.
> > Is there a better way?
> >
>
> You could probably use NAMD :-)
>
> Mark
>
>
> > Best,
> > Eric
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