Special options
So far all basic simulation options for PumMa have been discussed. However, now and then special requests to the simulation are needed, such as the fixing of atoms. In PumMa all these special options are listed in the special options file. By default this file is called specials.pif, but it can be set by the specfile option in the input file. Currently two special options can be set in the special options file:
Fixed atoms
In order to fix specific atoms during the course of the simulation, these atoms need to be specified in the special options file. Different levels of fixing are possible within PumMa. This can be one single atom, one molecule, all molecules of one type or one specific atom of one molecule type. Of course, combinations of these are also possible. For instance in a bilayer/water system to fix the fourth lipid molecule (DPPC), one specifies a line in the specfile that looks like
FIXED DPPC 4 *
where the first argument FIXED is again the keyword to tell the program that this lines holds information on the fixing of atoms, followed by the name of the type of molecule to be fixed. The third argument is the molecule number and the last argument (the wildcard symbol *) tells us that all atoms within this molecule should be kept fixed. If the line would have had two wildcards, so FIXED DPPC * *, all molecules of type DPPC would have been fixed.
On the other hand, if the fixfile contains lines that look like
FIXED DPPC * A3 FIXED DPPC * A4
the third and fourth atoms (those who are named A3 and A4 in the topology file) in all lipid molecules will be hold fixed. For this type of system this means that of each lipid molecule only two head atoms and all tail atoms are free to move, but not the atoms that connect the tails to the head part of the lipid.
A line of only wildcards causes the simulation to cease, since all atoms are fixed now and there is nothing to be simulated. A line without any wildcards, just a molecule type name, and two numbers specifies one particular atom in the system to be kept fixed, for instance FIXED DPPC 4 A2.
It is important to mention that whenever on any line in the specfile an atom is specified to be kept fixed, it cannot be set free again. This is particularly important when using wildcards and atoms might be specified fixed unexpectedly.
Separate heat baths
When using the Berendsen temperature coupling method normally all particles are coupled to the same heat bath. However, in some circumstances it can be necessary to decouple certain particle from the heat bath, while still coupling other particles. This can be done in PumMa by setting the sepheatbath option in the input file to on (the default is off). Subsequently PumMa tries to read the separate heat bath information from the specfile. Such a line might look like
SEPHB DPPC 300.0 0.005 SEPHB W 310.0 0.010
As can be seen, lines with respect to the separate heat bath start with the keyword SEPHB. In this example the lipids (DPPC) are kept at a temperature of 300 K, with a coupling constant (λc) of 0.005. Furthermore, water (W) is kept at 310 K with a λc of 0.0010. It must be noticed that the coupling to a heat bath always needs to be done at the molecule level.
Of course separate heat baths can also be used in conjunction with annealing. Each molecule can then be heated or cooled separately. In order to use this feature when has to set the annealing and sepheatbath option in the input file to on, and add several columns to the SEPHB lines in the specfile, which might then looks like
SEPHB DPPC 300.0 0.005 -0.1 500 270 SEPHB W 310.0 0.010 0.01 250 300
The first four arguments per line are still the same, but the next three are for the annealing, with the first (-0.1 and 0.01 in the example) are the equivalent of Trate in the input file. The second (500 and 250) are the Annrep for both molecules and the last column gives the Thold for the molecules.
Steered MD
Sometimes it is useful to control the motion of certain particles in the simulation. With Steered MD this is possible. In PumMa the constant velocity pulling method is implemented. In order to 'steer' a particle, an entry has to be supplied in the specfile, such as
STEER DPPC 50 A1 500.0 0.0 0.0 0.25
This line tells PumMa that atom A1 of the 50th DPPC molecule is to be steered (the first four arguments). In the constant velocity pulling method a pseudo particle is attached to the steered particle through a harmonic bond. The next argument of the steer entry inform PumMa about the force constant of the bond (here 500.0 kJ/nm2). The pseudo particle attached to the particle being steered is moved with a velocity specified by the last three arguments (the velocity components in x-, y- and z-direction, in nm/ps). Thus, in this example a pseudo particle attached to A1 of the 50th DPPC molecule is moved only in the z-direction with a speed of 0.25 nm/ps. The stability of the pulling depends heavily on the interplay of the force constant and the velocity of pulling. Initially, the pseudo particle is placed at a distance of the real particle, depending on the velocity of the pseudo particle, in such a way, that this distance functions as the reference length of the harmonic bond.
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