Dear GROMACS community,
evaluating the diffusivity of as single dodecyl sulfate (DS) anion, I
use a small trajectory chunk "md_00001.trr" 5 ps (500 frames) long for
testing purposes. The .trr has been stripped of any atoms except the 42
ones forming the DS chain (12H25SO4). What is more, I prepared an index
file DS_selection.ndx with the content
[ Surfactant ]
1 2 3 4 5 6 7 8 9 10 11 12 13
14 15
16 17 18 19 20 21 22 23 24 25 26 27 28
29 30
31 32 33 34 35 36 37 38 39 40 41 42
in order to select the molecule of interest explicitly. As far as I
understand the GMX 2016.4 manual and help, the commad
gmx msd -f md_00001.trr -s md.tpr -o atom_wise_msd.xvg -n
DS_selection.ndx
should yield the atom-wise evaluated MSD averaged over all 42 atoms for
each timestep. "atom_wise_msd.xvg" contains the comment
....
# MSD gathered over 4.99 ps with 1 restarts
# Diffusion constants fitted from time 0.5 to 4.49 ps
# D[Surfactant] = 1.8305 (+/- 1.3704) (1e-5 cm^2/s)
....
which I understand as the atom-averaged diffusivity. On the other hand,
gmx msd -f md_00001.trr -s md.tpr -o mol_wise_msd.xvg -mol
mol_wise_D.xvg -n DS_selection.ndx
should yield MSD (and diffusivity D) for the molecule's COM, and
consequently a different value D
....
# MSD gathered over 4.99 ps with 1 restarts
# Diffusion constants fitted from time 0.5 to 4.49 ps
# D[Surfactant] = 1.5575 (+/- 1.3521) (1e-5 cm^2/s)
....
is found within "mol_wise_msd.xvg". So far, so good, my understanding is
correct up until here?
Now, looking at the latter command's stdout, I have
<D> = 1.1395 Std. Dev. = -nan Error = -nan
Fitting from 0.5 to 4.49 ps
D[Surfactant] 1.5575 (+/- 1.3521) 1e-5 cm^2/s
and in the file "mol_wise_D.xvg" of course just one entry for the single
DS molecule
....
@ title "Diffusion Coefficients / Molecule"
@ xaxis label "Molecule"
@ yaxis label "D"
@TYPE xy
0 1.13953
Here, I am confused. How does the third value for D arise? Naturally, I
would have expected "mol_wise_D.xvg" to list the same value of D =
1.5575 as found within the comment of "mol_wise_msd.xvg".
I am looking forward to a clarifying answer, as I could not find any
notes on this discrepancy in the documentation. Is it maybe possible
that the <D> = 1.1395 is evaluated over all 5ps, whereas D[Surfactant] =
1.5575is fitted only on the 80% trajectory from 0.5 to 4.49 ps? If so,
some clear hint towards this fact would be appreciated in the "gmx help
msd" text.
A different topic: I could not find any option for "gmx msd" to evaluate
a trajectory frame-wise without loading the whole file into memory. When
applied onto a several GB .trr, even with relatively small "-trestart”，
GMX would continuously eat up memory until the job would be canceled due
to running out of the node's 128 GB RAM. Maybe any undocumented option
hidden somewhere?
Here the output of "gmx --version"
GROMACS: gmx, version 2016.4
Executable:
/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/gromacs_2016.4_gnu/bin/gmx
Data prefix:
/work/ws/nemo/fr_lp1029-IMTEK_SIMULATION-0/gromacs_2016.4_gnu
Working dir:
/work/ws/nemo/fr_jh1130-201708-0/jobs/gmxlab/sds/201801/farafonov2017developing/1ds/rtp/GAFF-SPC
Command line:
gmx --version
GROMACS version: 2016.4
Precision: single
Memory model: 64 bit
MPI library: thread_mpi
OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32)
GPU support: disabled
SIMD instructions: AVX2_256
FFT library: fftw-3.3.7-sse2-avx-avx2-avx2_128
RDTSCP usage: enabled
TNG support: enabled
Hwloc support: hwloc-1.11.0
Tracing support: disabled
Built on: Wed Dec 13 10:46:41 CET 2017
Built by: fr_jh1...@int02.nemo.privat [CMAKE]
Build OS/arch: Linux 3.10.0-693.5.2.el7.x86_64 x86_64
Build CPU vendor: Intel
Build CPU brand: Intel(R) Xeon(R) CPU E5-2630 v4 @ 2.20GHz
Build CPU family: 6 Model: 79 Stepping: 1
Build CPU features: aes apic avx avx2 clfsh cmov cx8 cx16 f16c fma
hle htt lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt
pse rdrnd rdtscp rtm sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic
C compiler: /opt/bwhpc/common/compiler/gnu/5.2.0/bin/gcc GNU 5.2.0
C compiler flags: -march=core-avx2 -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
C++ compiler: /opt/bwhpc/common/compiler/gnu/5.2.0/bin/g++ GNU 5.2.0
C++ compiler flags: -march=core-avx2 -std=c++0x -O3 -DNDEBUG
-funroll-all-loops -fexcess-precision=fast
Thanks for your help.
Best regards,
--
Johannes Hörmann
University of Freiburg
IMTEK - Department of Microsystems Engineering
Laboratory for Simulation
Georges-Köhler-Allee 103, Room 03 020
79110 Freiburg, Germany
Office: +49-761-203-67726
Email: johannes.hoerm...@imtek.uni-freiburg.de
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