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

Yun Shi yunshi09 at gmail.com
Sun Sep 9 00:26:55 CEST 2012

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.

But what could be an alternative way to look at the system evolution upon
reduction of the co-factor?


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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