On 9/09/2012 8:09 AM, Yun Shi wrote:
Hi everyone,
I am running MD of an enzyme containing co-factor FADH2.
After the enzyme stabilize, I want to reduce the FADH2 to FAD, which for me
is to delete two H atoms and change the topology file and .gro file
correspondingly.
However, I want to continue the MD run with the state (velocities,
temperature, pressure...) right before the reduction (deletion of 2 H
atoms), which requires .cpt file. How could I match the .cpt file with the
new structure that has 2 H atoms deleted?
You can't. There's no sense in which the two would be continuous, and as
far as I can see little virtue in seeking it. It might be possible to
convert the .cpt to a .trr and form the correct subset, projecting the
missing velocities properly, etc. which could be given to grompp with a
new .top... but what's the point?
Mark
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