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

[Yun Shi]

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?

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
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>