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 <[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 > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
