[gmx-users] Convert-tpr pbc problem for membrane protein

[Justin Lemkul]

On 4/16/15 3:11 PM, wh wrote:
> Dear Gromacs users,
>
>
>
> I recently used Charmm-gui Gromacs input generator to build some input files
> for a membrane protein system and ran several simulation with them.
> Recommended by charmm-gui README file I used convert-tpr to perform
> continuous simulation. Thus the trajectory itself will have some crazy
> behavior, with protein in parts and lipid deformed. I managed to restore the

I don't see how using convert-tpr (which is the normal way to extend a run) will 
inherently lead to "crazy behavior."

> protein and generate a trajectory with just protein. However, now I have a
> problem to  transform the whole system including lipid and water, ions. No
> matter what I tried the lipid will still have a bizarre shape. Does anyone
> have experience with this issue? Any suggestion will be greatly appreciated.

You'll have to provide some actual commands of what you're doing to deal with 
periodicity and likely upload some images of what you're defining as "bizarre 
shape."  If the molecules were actually distorted, the simulation would have 
crashed.  Likely whatever you're doing with trjconv is wrong.  Note that the 
CHARMM convention is to center the system at the coordinate origin, whereas in 
GROMACS the center is (x/2, y/2, z/2).  So you have to generate a properly 
centered reference state before doing anything else.  There will be several 
steps to the process, but it is perfectly possible to re-image a trajectory run 
with a CHARMM-GUI starting structure; we do it routinely.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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