用ptraj成像

The box we created with packmol manifests a fundamental problem: a significant portion of the molecules is exposed to vacuum, which would yield deviations in simulation results. Under periodic boundaries, our box is “replicated” in all three dimensions so that our system represents a realistic bulk fluid. As a result, when a molecule exits the box from one side, it enters from the other. Ptraj's imaging tool repacks the molecules that left the box and gives us a proper image of what the central box looks like.

Create an input file, “ptraj.in”:

                trajin md1.nc # the name of the trajectory
              
                image center
              
                trajout ptraj.out # the name of the output filethe

To run ptraj, run the following command:

                ptraj prmtop ptraj.in
              

Ptmtop is the topology file for our box.

image: 10_Users_case_projects_ionic_liquids_mdionic2.jpg

image: 11_Users_case_projects_ionic_liquids_image.jpg

Figure 9:

MD results: (left) before imaging in ptraj; (right) after imaging

Radial Distribution Functions (RDFs)

First, analyze the Density to see if the average density is close to your target.

awk '/Density/ { print $3 }; $1=="A" && $2=="V" {exit 0}' md1.out > density.dat

This awk script takes in the input file (md1.out) and prints the third column everytime the word “Density” appears in a line. The output is channeled into “density.dat”. When awk reaches the “Average” section in the output file, the script quits.
To graph density data with xmgrace:

$ xmgrace density.dat
To calculate the average density, examine the sets in xmgrace, or run the following script:

awk '{ sum = sum + $1 }; END { print "average = ", sum/NR }' density.dat

This awk script takes in density.dat, and adds the first column of each line to “sum”, then prints sum divided by NR (a special variable for Number of Records).
Examine the Energy Total to see if the system is at equilibrium.

awk '/Etot/ {print $3}; ($1=="A" && $2=="V") {exit 0};' Eq2.1.out > etot.dat

To graph the Energy Total data in xmgrace, use commands similar to those above for the density.

Below is an example of the graph of the Energy Totals for the the MD simulation for the ionic liquid mixture of [bmim][BF4] and acetonitrile:
Once the density is at target and total energy is at equilibrium, calculate Radial Distribution Functions.
1. In this case, the average density is 1.0774 cc/mol, whereas the paper's density is 1.087 cc/mol.

image: 12_Users_case_projects_ionic_liquids_Densitytutorial.jpg

image: 13_Users_case_projects_ionic_liquids_Etottutorial.jpg

Figure 10:

Time dependence of the density (left) and total energy (right)

In order to calculate the RDFs, we will use ptraj, a program used to analyze sets of 3-D coordinates from input coordinate files. We will be calculating the RDF between the N1 atoms of the Acetonitrile [CH3CN]

1) Create an input file ptraj.in

                trajin <trajectory filename>
              
                radial CH3CN_N1 .1 15.0 :ACN@N

2)Run

                ptraj prmtop ptraj.in
              

CH3CN_N1 is the header for output file names, .1 is the bin size, 15.0 is the maximum for the histogram, and :ACN@N is the mask for selecting atoms we want to use for our analysis.

The output files that result after running the ptraj.in file will be: CH3CN_N1_carnal.xmgr CH3CN_N1_standard.xmgr CH3CN_N1_volume.xmgr

Use Xmgrace to open the files to view the resulting graph of the RDFs. For example:

                $ xmgrace CH3CN_N1_volume.xmgr
              

The above command will open the file CH3CN_N1_volume.xmgr in xmgrace. The x axis is distance in angstroms, and g(r) gives the probablity of finding an atom (in this case, the nitrogen in acetonitrile) at a given distance (r) of another atom (another nitrogen in acetonitrile). The first peak (around four angstroms) represents the first coordination shell, and the second peak (little less than six angstroms) represents the second coordination shell.

image: 14_Users_case_projects_ionic_liquids_rdfcrof25ns.jpg

Figure 11:

Radial distribution function

产品

会议

学习

关于 ILPlatform