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
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