I am interested in comparing absorption spectrum from Amber to experimental
data. The procedure I use is: .mdcrd/trajectory file -> ptraj -> .mode ->
Matlab ->absorption coefficient vs frequency. I am using Amber 8, ff03,
ifort 8, on an old Fedora machine (Fedora 3 I think, so a single computer).
I was seeing variability of my absorption coefficients based on: simulation
time, translation removal interval, integration step and basically any other
parameter I changed.
So I performed the following production runs (as described in the tutorial I
have performed 20ps of NVT to reach 300K, and 100ps NTP to reach ~1gm/cm^3):
-100ps simulation time, 2fs integration step, NPT, translation removed every
2fs
-100ps simulation time, 2fs integration step, NPT, translation removed every
10fs
-100ps simulation time, 2fs integration step, NPT, translation removed every
50fs
-100ps simulation time, 2fs integration step, NPT, translation removed every
100fs
-100ps simulation time, 2fs integration step, NPT, translation removed every
200fs
-100ps simulation time, 2fs integration step, NPT, translation removed every
1000fs
-100ps simulation time, 2fs integration step, NPT, translation removed every
2000fs
-100ps simulation time, 2fs integration step, NVE, translation removed every
2fs
-100ps simulation time, 2fs integration step, NVE, translation removed every
10fs
-100ps simulation time, 2fs integration step, NVE, translation removed every
100fs
-100ps simulation time, 2fs integration step, NVE, translation removed every
200fs
The result of every experiment was different, however when each set was
average they produced almost the same result, and this absorption spectra
was very close to the experimental data. The NVE results seemed to represent
the experimental data better (I can sent the plots).
There seems to be some source of noise in the system. The noise is large
enough to mask the results until averaging cancels out the random noise. For
NPT the temperature is adjusted every 1ps (tautp) and the pressure is
changed every 2ps (taup). This, in addition with the translation removal
could be the culprit. In the NVE simulation, I did not find anything being
adjusted other than the translation removal (since I could not find anything
in the manual I am assuming the volume is kept constant by not touching the
unit cell). Therefore, I tried simulating in NVE regime w/ no translation
removal (also in this amber archive discussion
http://archive.ambermd.org/200803/0158.html). However the noise is still
there. In the archives there was a concern about the tolerance of parameters
used to calculate long distance interactions during NVE (
http://archive.ambermd.org/200708/0145.html). I have not tried these
recommendations but I am not sure how it would help since my total energy
changes by .02% during the 100ps simulation. Also based on the RMS data, my
structure moves ~1 angstrom during the 100ps production simulation and my
cell size is ~50 (angstroms)^3.
The only other disturbance I could think in NVE is the SHAKE procedure used
to constrain hydrogen vibrations. However, there seems to be multiple views
about what happens when SHAKE is turned off. In these discussions a very
short time step ~1fs or .25fs is recommended (
http://archive.ambermd.org/200102/0132.html,
http://archive.ambermd.org/200312/0256.html,
http://archive.ambermd.org/200605/0407.html)
However at the same time in this discussion (
http://archive.ambermd.org/200508/0125.html) it is mentioned that "Amber
force fields are not really designed to give proper dynamics for bonds
involving hydrogen. In fact one of the reasons to constrain them is that
they really are not described well by classical potentials." Does this mean
that using TIP3P or SPC model w/o SHAKE would be meaningless anyways?
Because the large van der Waal centered on oxygen atom facilitates hydrogen
bonds only between water molecules and not between water and solute i.e.
hydrogens from one water molecules would fly off and cluster around the
oxygen atom of another water molecule?
I will eventually upgrade to Amber 10 and try SPCFW w/ ff99SB, but I was
wondering what are possible disturbance during NVE simulation? Or are there
any other suggestions for creating the system with minimal disruptions
during production run?
Thanks in advance
Naser
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Received on Fri Oct 03 2008 - 05:07:45 PDT
