[gmx-users] yet another question about PBC...

[Tsjerk Wassenaar]

Hi,

use trjconv

Well, that's just to start the mail with it in stead of ending. g_rms
(g_gyrate, g_rmsf, g_covar) are rather dumb programs, taking a
structure, fitting it to a reference orientation and doing some stuff
on it. They don't check for jumps over the PBC. PBC and fitting don't
go too well together (check some other posts of mine about trjconv,
fitting and pbc in the FML). It's best to do that automatically using
trjconv when your run has finished.

As for the warning, Justin is completely right, but I might add
explicitly that that warning has nothing to do with jumping subunits.

Hope it helps,

Tsjerk

On Mon, Jun 30, 2008 at 5:26 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Ramon Crehuet wrote:
>>
>> Hi,
>> Please don't flame me for asking yet another question about the "out of
>> the box" and PBC issue. I've tried to RTFM, RTFML, but could not find
>> the question I'm asking.
>> I (think) I understand what PBC implies and the fact that "out of the
>> box" makes no sense because the system is periodic and gromacs treats
>> the periodicity correctly. However, when calculating the rmsd of a
>> trajectory with g_rms with respect to the protein I get a warning:
>> "cannot make broken molecules whole without a run input file, don't
>> worry mdrun doesn't write broken molecules".
>> and the rmsd has unrealistic jumps when the chains of the protein (a
>> tetramer) leave the box (but if I calculate distances with g_bond, they
>> are always ok)
>> If I correct the trajectory with trjconf -pbc nojump, the new trajectory
>> seems to behave as expected.
>> So my questions are, i)should I worry about the warning? ii) why does
>> g_rms not treat PBC as expected? Should I use some options?
>>
>
> As far as the warning, it's due to the fact that you specified something
> like a .pdb or .gro file for the -s flag, and not the .tpr file.  Not so
> important in this case, but it would affect, for example, making molecules
> whole with trjconv.
>
> As for the second part, perhaps someone else has better insight, but usually
> the quick answer is to compensate for PBC using trjconv, as you have.  I
> know there are a few messages about this in the list archives, but I think
> they usually end with "use trjconv."
>
> -Justin
>
>
>> Thanks in advance,
>> Ramon
>>
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>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623