[gmx-users] Gradually increasing the force constant during restrained MD runs

[chris.neale at utoronto.ca]

Dear Aditi:

you can do this by scripting gromacs to run in short segments,  
modifying the force constant for each run. e.g.:

#!/bin/bash
for((i=1;i<=100; i++)); do
   let "j=i-1"
   grompp -f ${i}.mdp -p ${i}.top -f ${j}.gro -o ${i}.tpr
   mdrun -deffnm ${i}
done

You only need to use some more scripting to create the ${i}.top and  
${i}.mdp files, although I think that orientational restraints are  
going to be part of the topology so the .mdp file can even remain  
constant.

You can then trjcat -settime once you are done.

-- original message --

I am running an MD simulation on RNA with orientation restraints.  
Instead of using a single force constant for the whole trajectory, I  
want to start with a very low force constant and increase it gradually  
and regularly up to a final suitably high value and then continue the  
simulation at this final value of force constant.

Can you suggest if there is a way to do so in GROMACS?

Thanks!

Aditi