[gmx-users] How to delete atoms during MD runs?

[Mark Abraham]

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