[gmx-users] MD exit condition

Mark Abraham mark.j.abraham at gmail.com
Thu Aug 28 15:58:19 CEST 2014

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 :-)


> Best,
> Eric
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