On 3/27/14, 1:54 PM, João Henriques wrote:
Thanks Justin. That corroborates my "no .tpr, no party" suspicion. However,
would it be possible to achieve a correct analysis if I were to use a whole
.gro with a properly pre-processed .xtc (-ur -pbc)? Maybe I didn't explain
myself properly, but that's what I want to know.
Yes, if you have removed jumps and have intact structures throughout the
trajectory, you're fine. The warning is only there for users who haven't
thought ahead.
-Justin
/J
On Thu, Mar 27, 2014 at 6:32 PM, Justin Lemkul <jalem...@vt.edu> wrote:
On 3/27/14, 1:27 PM, João Henriques wrote:
Hello everyone,
The documentation reads:
"""
All structures are fitted to the structure in the structure file. When
this
is not a run input file periodicity will not be taken into account.
"""
This is rather cryptic, what does it mean in practice? No tpr, no party?
What if I use a properly centered and whole .gro file?
When ran with a .gro as the structure input file, I get two warnings. One
is related to the masses, which are non-existent in the .gro, but I don't
need them anyway. The second warning is honestly confusing me even more.
"""
WARNING: If there are molecules in the input trajectory file
that are broken across periodic boundaries, they
cannot be made whole (or treated as whole) without
you providing a run input file.
"""
The documentation points out to the structure input file and now it's the
trajectory? What's going on? Do I also need to make each frame whole in
the
input .xtc? Can someone elaborate on this?
The documentation consistently refers to the run input file. A .tpr has
record of how periodicity is treated. Nothing else does. If you don't
tell g_covar (like most Gromacs tools) how periodicity is treated, you can
get garbage as a result. The trajectory may have "broken" molecules,
because mdrun doesn't care how they look - it has a run input file and thus
knowledge of periodicity. When running analysis like g_covar, if the
bonded connectivity of the molecule and the periodicity are unknown (again,
if you're not using a .tpr), then absolute displacements of coordinates are
used, thus your analysis might be totally hosed if the molecule "splits" -
that would be a rather dramatic structure change detected by g_covar. In
fact, so dramatic that it's false.
-Justin
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==================================================
Justin A. Lemkul, Ph.D.
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Department of Pharmaceutical Sciences
School of Pharmacy
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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