On 9/09/2012 8:26 AM, Yun Shi wrote:
Hi Mark,
I just want to look into the conformational change of the enzyme after
reduction of the co-factor FAD. So instead of feed into a reducing molecule
and do some complicated QM simulation, I wonder if this way would be
better. I understand that this is not physical.
You can't say anything about the conformational change unless you've
sampled both ensembles pretty well, which in principle should be
independent of both initial conditions. Hence not bothering much about them.
But what could be an alternative way to look at the system evolution upon
reduction of the co-factor?
There are alchemical free-energy methods that let you convert one to the
other mid-simulation with just an MM model, but that doesn't seem to
suit what you want to do.
Mark
Thanks,
Yun
On Sat, Sep 8, 2012 at 3:17 PM, Mark Abraham <[email protected]>wrote:
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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