On 3/30/18 7:29 AM, jt555 wrote:
Hello there,
I am currently using GROMACS version 5.1.2 and had a question in relation to
the gmx check command. The following appears on the screen after invocation of
gmx check -f protein.pdb:
GROMACS: gmx check, VERSION 5.1.2
Executable: /usr/bin/gmx
Data prefix: /usr
Command line:
gmx check -f protein.pdb
Checking file protein.pdb
Reading frame 0 time0.000
# Atoms 9190
Precision 0.0001 (nm)
'GROtesk MACabre and Sinister t= 40.0', 9190 atoms
Reading frame6000 time 24.000
Item#frames Timestep (ps)
Step 625040
Time 625040
Lambda 0
Coords625040
Velocities 0
Forces 0
Box 0
The precision = 0.001 nm, all my attempts at locating the answer for my
questions proved futile.
Question) Invocation of similar command for XTC file (i.e., gmx check -f
protein.xtc) also results in precision of 0.001 nm. However, in the manual it
clearly states that .xtc exhibits greater precision in comparison to .pdb. If
Where does it say that?
that is the case, then why am I observing the same value for precision in both?
Or is it the case that because the
The default precision for an .xtc file is exactly what you're seeing,
unless you're changing it in the .mdp file to save more decimal places.
system under investigation only contains 9,190 atoms, therefore the difference
in precision between .xtc and .pdb is almost negligible and only realised when
a much larger system is under investigation? FInally, could you kindly
The precision of output files is not related to the size of the systems.
summarise the significance of precision obtained from gmx check command for a
beginner?
It's just reporting how many decimal places are saved.
-Justin
I thank you in advance for your kind assistance.
Yours faithfully,
J.
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--
==
Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
==
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