Molecular Dyamics Simulations¶
In this chapter, all necessary information will be given in order to perform MD simulations with xTB. The adjustable parameters will be discussed and a guide to how to change them will be given.
Contents
General command-line control¶
There are two main possibilities how to evoke a MD simulation.
With the flag --omd
geometry optimization will be performed
and this structure then will be used for the MD simulation, a loose
optimization level will be chosen.
> xtb coord --omd
By using the flag --md
the MD simulation will be performed directly with the user given input structure.
> xtb coord --md
It is strongly recommended to start the MD simulation from an xTB optimized structure. Otherwise there may be instabilities during the MD and the equilibration will be severely hindered.
Parameters¶
In order to change the parameters of the MD simulation the $md
block
in the input file has to be modified.
key
value
default
description
dump
real
50 fs
interval for trajectory printout
hmass
integer
4 times
mass of hydrogen atoms
nvt
boolean
true
perform simulation in NVT ensemble
restart
boolean
false
read velocities from
mdrestart
temp
real
298.15 K
thermostat temperature
time
real
50 ps
total run time of simulation
sccacc
real
2.0
accuracy of xTB calculation in dynamics
shake
integer
2
use SHAKE algorithm to constrain bonds
0 = off, 1 = X-H only, 2 = all bonds
step
real
4 fs
time step for propagation
velo
boolean
false
also write out velocities
The above default setting should look like below in your input file
$md
temp=298.15 # in K
time= 50.0 # in ps
dump= 50.0 # in fs
step= 4.0 # in fs
velo=false
nvt =true
hmass=4
shake=2
sccacc=2.0
$end
Important
For MD simulations with GFN-FF the time step must be reduced, for more information see section GFN-Force-Field (GFN-FF)
MD specific Files¶
After the xtb
program has performed the desired MD simulation the trajectory of the structures can be found in xtb.trj
.
Furthermore, files with the names scoord.*
are generated. After every picosecond of simulation the structure at this point will be written into these files. After a successful completion of the MD simulation a xtbmdok
file will be touched. The structure and velocities at the end of the simulation will be written into a mdrestart
file.
Trajectory¶
The number of structures in the xtb.trj
file depends on the dump
variable and the propagation time step.
For practical purposes the two parameters are converted into a dump frequency n = (dump step/time step), e.g.,
a structure is written to the trajecotry equidistantly at every n-th propagation step.
Due to this conversion the total number of structures in the xtb.trj
file might be slightly larger
than the expected (total runtime/dump step).
The same applies to the scoord.*
files.
Restart¶
The mdrestart
file can be used to restart an MD simulation. This can be very helpful for equilibration purposes.
In order to achive this, in the $md
block the restart
parameter has to be set to true
.
> cat restart.inp
$md
restart=true
Example/Case study¶
To summarize the most important topics of this chapter we will perform an MD simulation of the ethane molecule with xTB.
Make sure that xtb
is properly set up and you have the following files in your working directory
> cat coord
$coord
1.82409443250962 -0.02380488009596 0.17250251620479 c
4.68095348739630 -0.02380488009596 0.17250308312263 c
1.09744635742609 1.41159121722257 -1.12629926294082 h
1.09744579050825 0.38329239564274 2.06499275150500 h
1.09744635742609 -1.86629844212581 -0.42118612892243 h
5.40760175145245 1.81868868193389 0.76619172824984 h
5.40760212939767 -0.43090215583466 -1.71998734115020 h
5.40760175145245 -1.45920097741449 1.47130486226824 h
$end
> cat md.inp
$md
time=10
step=1
temp=500
shake=1
As you can see, we will run the simulation for 10 ps with a timestep of 1 fs at a temperature of 500 Kelvin. Furthermore, all hydrogen-containing bonds will be constrained using the SHAKE algorithm. To start the simulation we call xtb as follows
> xtb coord --input md.inp --omd
The program will start with performing a geometry optimization,
the optimized structure used to start the dynamic can be found
and inspected in xtbopt.coord
.
In the file xtb.trj
we can find our trajectory. We can analyze the structures now by displaying them in a molecular graphics editor (e.g., MOLDEN, VMD etc. ) or a trajectory analyzer (e.g. TRAVIS).