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

wh signoreguidami at 163.com
Fri Apr 17 03:58:12 CEST 2015

Gromacs shrink the box in x and y direction and prolong in z direction when
recording the trajectory. And when loading the trr files directly I can see
the lipid is wrapped.  Based on some analysis of the protein I think the
simulation is fine and it should be just a visualization problem. My system
is not symmetric in z direction, with the position of the lipid higher than
the initial box center. Do you have any idea how to fix it? Or usually how
would you deal with the trajectory of charmm-gui?

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



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


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