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

[Justin Lemkul]

On 4/16/15 9:57 PM, wh wrote:
> 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

By how much?  Does the effect level off?  The initial configuration and box 
dimensions will change as a function of the run settings and force field.

> 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?
>

Symmetry doesn't matter (it's actually irrelevant with PBC).  But again, you're 
going to have to provide real details of what you're dealing with and what 
you're doing, per my questions below.  The exact approach depends on what you 
have.  Single protein?  Complex?  What steps have you taken to re-image?  What's 
"wrong" about them?  Post your exact sequence of commands and share some images.

-Justin

>
>
> 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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