Dear Collagues,
We are having a question relating to our MD simulations, in which we
connect a gold nanoparticle (Au NP) with a drug-binding peptide and
the corresponding drug molecule. The peptide is bound via a cysteine
residue to the Au NP and here the corresponding bonded interactions,
angles and dihedrals between Au and S have been assigned in the
ffbonded.itp file. In the same way, we proceeded with the non-bonded
interactions between the Au atoms in the ffnonbonded.itp file. When we
started to heat our system, the Au NP was disintegrating, i.e. the
non-bonded interactions between the Au atoms are not sufficient to
keep the NP together. Therefore, we considered position restraints for
all Au atoms that we maintained during heating, relaxation and
production phase (NPT). Since pressure coupling with absolute position
restraints requires refcoord-scaling, we applied the
refcoord-scaling=com option in the mdp-file.
The simulations performed are stable, run without any further problems
relating to disintegration of the Au NP and we obtain reasonable
results. However, there is one problem, namely as soon as we want to
extract information from the production phase relating to the Au atoms
between two subsequent MD runs (simply extending the time under the
same conditions in the second MD run), we observe an artificial jump
in certain quantities, for instance when calculating the RMSD, the
radius of gyration or the solvent accessible surface area with respect
to the Au atoms with position restraints. As long as we calculate
these properties in a single MD run, these quantities are stable (of
course fluctuating, but without any artificial jumps).
We ascribe the observed artificial jump that is always occurring at
the very beginning of the extended MD run to the rescaling of the com.
We tried different approaches to get rid of this physically not
meaningful jump by combining the trajectories of subsequent MD runs
(gmx trjcat) and then calculate these properties with respect to the
Au atoms or by calculating the center of mass (com) for the Au atoms
in the NP for both simulations and then translating the ?new com?
(first frame in the extended MD simulations) to the ?old com? (last
frame in the first MD run). Both approaches were not successful, still
the artificial jump is occurring. We also tried to adjust the
reference (for ?-s? in the commands we applied various tpr- and
gro-files), but this is also not the solution of the problem.
Does anyone have had the same or a similar problem or even better does
someone know how to get rid of this issue without virtually shifting
the output data of the subsequent MD run towards the output data of
the first MD run?
Any help is appreciated. Thanks a lot for your efforts in advance.
With my best regards,
Kai
P.S.: We also outlined that the observed jump is indeed artificial,
namely by taking an extended MD simulation and running it from the
original starting point directly for the double time. In that case, no
artificial jump occurs.
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