[gmx-users] Replacing a residue and continuing a simulation run
tsjerkw at gmail.com
Wed Mar 16 06:22:09 CET 2011
I'd say that if the changes are small you should be able to get away
with it. You might want to start off the second part of the run with a
smaller time step to relax, though. If the change is from TRP to TRP*,
you only need to have a modified topology, without touching the
coordinates. You do need to set up a new .tpr file from the the .trr
and the modified topology.
Hope it helps,
On Tue, Mar 15, 2011 at 10:11 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> J. Nathan Scott wrote:
>> Hello all,
>> I was wondering, is it possible to replace a residue and then continue
>> a simulation using the new parameters/geometry of the new residue? The
>> reason I ask is that I am interested in performing simulations of
>> proteins with tryptophan in its excited state following a lengthy
>> equilibration with TRP in its ground state. I already have reliable
>> excited state atomic charges for the TRP atoms, and I suppose that I
>> will need to change at least some bonded terms to account for the
>> altered geometry of the excited state.
>> I am still in the middle of reading the information that is out there
>> regarding parameterizing new molecules (since I'm using the CHARMM FF,
>> I've been starting to follow Alexander MacKerell's protocols), but I'm
>> still not quite sure as to how one would practically do this residue
>> replacement in the context of a Gromacs run. Will I need to manually
>> edit my .top file, or is there perhaps another way to update the
>> topology file with the new residue following the ground state
>> equilibration? How about coordinates, will I need to transform the TRP
>> coordinates to the excited state geometry by hand?
> You would have to hack the topology. Coordinates are another matter. If
> you start making ad hoc changes, then what's the point of a continuation?
> Presumably, if you've designed the residue's topology correctly (including
> both bonded and nonbonded parameters), then the residue will adopt the
> correct geometry on its own.
> The complication comes with bonded interactions. Are you using constraints?
> If so, then changing bond lengths will cause the constraints to fail at
> step 0 (or very soon thereafter) and the simulation will crash. You can get
> around this by setting "continuation = no" in the .mdp file, but again I
> wonder what the value of the continuation is. You'd almost certainly have
> to forgo the use of .cpt files, supplying instead your .trr and .edr files
> to preserve as much of the previous ensemble as possible. Even if you're
> not using constraints, the simulation may still fail if you're suddenly
> changing bond lengths, angles, etc by anything more than a very small
>> Perhaps the most important question: is there a better way to do the
>> sort of residue replacement I'm contemplating, or is this something
>> that is just inherently going to be a bit messy?
> I can't see any way around topology hacking. If you need different
> parameters, you need a different topology. It's going to be a bit messy,
> and I would encourage you to give some serious thought to the potential
> pitfalls I listed above.
>> Thanks very much for any insight or guidance you can offer!
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> gmx-users mailing list gmx-users at gromacs.org
> 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Tsjerk A. Wassenaar, Ph.D.
Molecular Dynamics Group
* Groningen Institute for Biomolecular Research and Biotechnology
* Zernike Institute for Advanced Materials
University of Groningen
More information about the gromacs.org_gmx-users