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

Mark Abraham Mark.Abraham at anu.edu.au
Sun Sep 9 00:35:08 CEST 2012

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.


> Thanks,
> Yun
> On Sat, Sep 8, 2012 at 3:17 PM, Mark Abraham <Mark.Abraham at anu.edu.au>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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