Shortcut: READMASSCHARGE

Module generic
Description Usage
Set the masses and charges from an input PDB file. used in 0 tutorialsused in 0 eggs

Output components

This action calculates the values in the following table. These values can be referenced elsewhere in the input by using this Action's label followed by a dot and the name of the value required from the list below.

Name Type Description
mass vector the masses of the atoms in the system
charges vector the masses of the atoms in the system

Further details and examples

Set the masses and charges from an input PDB file.

You can use this command to read in the masses and charges for the atoms as shown in the example input below:

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS INPUTFILES=regtest/basic/rt-readmasscharge2/mcinpt
mq: READMASSCHARGESet the masses and charges from an input PDB file. This action is a shortcut. More details FILEinput file that contains the masses and charges that should be used=
regtest/basic/rt-readmasscharge2/mcinpt
Click here to see an extract from this file.
×

FILE: regtest/basic/rt-readmasscharge2/mcinpt

#! FIELDS index mass charge
 0                      1                      1
 1                      2                      0
 2                      3                      1
 3                      2                      0
 4                      1                      1
 5                      2                      0
 6                      3                      1
 7                      2                      0
 8                      1                     10
 9                      2                      0
 10                      3                     20
 11                      1                      1
 12                      1                      1
 13                      1                      1
 14                      1                      1
 15                      1                      1
 16                      1                      1
 17                      1                      1
 18                      1                      1
 19                      1                      1
 20                      1                      1
 21                      1                      1
 22                      1                      1
 23                      1                      1
 24                      1                      1
 25                      1                      1
 26                      1                      1
 27                      1                      1
 28                      1                      1
 29                      1                      1
 30                      1                      1
 31                      1                      1
 32                      1                      1
 33                      1                      1
 34                      1                      1
 35                      1                      1
 36                      1                      1
 37                      1                      1
 38                      1                      1
 39                      1                      1
 40                      1                      1
 41                      1                      1
 42                      1                      1
 43                      1                      1
 44                      1                      1
 45                      1                      1
 46                      1                      1
 47                      1                      1
 48                      1                      1
 49                      1                      1
 50                      1                      1
 51                      1                      1
 52                      1                      1
 53                      1                      1
 54                      1                      1
 55                      1                      1
 56                      1                      1
 57                      1                      1
 58                      1                      1
 59                      1                      1
 60                      1                      1
 61                      1                      1
 62                      1                      1
 63                      1                      1
 64                      1                      1
 65                      1                      1
 66                      1                      1
 67                      1                      1
 68                      1                      1
 69                      1                      1
 70                      1                      1
 71                      1                      1
 72                      1                      1
 73                      1                      1
 74                      1                      1
 75                      1                      1
 76                      1                      1
 77                      1                      1
 78                      1                      1
 79                      1                      1
 80                      1                      1
 81                      1                      1
 82                      1                      1
 83                      1                      1
 84                      1                      1
 85                      1                      1
 86                      1                      1
 87                      1                      1
 88                      1                      1
 89                      1                      1
 90                      1                      1
 91                      1                      1
 92                      1                      1
 93                      1                      1
 94                      1                      1
 95                      1                      1
 96                      1                      1
 97                      1                      1
 98                      1                      1
 99                      1                      1
 100                      1                      1
 101                      1                      1
 102                      1                      1
 103                      1                      1
 104                      1                      1
 105                      1                      1
 106                      1                      1
 107                      1                     10

In the above example the masses and charges are in a file called mcinpt that contains three columns of numbers. The first column of numbers is a numerical index, the second column is the masses and the third is the charges.

You can read masses and charges from a PDB file instead by using an input like the one shown below:

Click on the labels of the actions for more information on what each action computes
tested on2.11
#SETTINGS NATOMS=108 INPUTFILES=regtest/basic/rt-readmasscharge/test.pdb
mq: READMASSCHARGESet the masses and charges from an input PDB file. This action is a shortcut. More details PDBFILEa pdb file that contains the masses and charges of the atoms in the beta and occupancy columns=
regtest/basic/rt-readmasscharge/test.pdb
Click here to see an extract from this file.
×

FILE: regtest/basic/rt-readmasscharge/test.pdb

ATOM      1  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM      2  Ar                  0.000   0.000   0.000  2.00  0.00
ATOM      3  Ar                  0.000   0.000   0.000  3.00  1.00
ATOM      4  Ar                  0.000   0.000   0.000  2.00  0.00
ATOM      5  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM      6  Ar                  0.000   0.000   0.000  2.00  0.00
ATOM      7  Ar                  0.000   0.000   0.000  3.00  1.00
ATOM      8  Ar                  0.000   0.000   0.000  2.00  0.00
ATOM      9  Ar                  0.000   0.000   0.000  1.00 10.00
ATOM     10  Ar                  0.000   0.000   0.000  2.00  0.00
ATOM     11  Ar                  0.000   0.000   0.000  3.00 20.00
ATOM     12  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     13  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     14  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     15  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     16  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     17  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     18  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     19  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     20  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     21  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     22  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     23  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     24  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     25  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     26  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     27  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     28  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     29  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     30  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     31  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     32  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     33  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     34  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     35  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     36  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     37  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     38  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     39  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     40  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     41  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     42  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     43  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     44  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     45  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     46  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     47  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     48  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     49  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     50  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     51  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     52  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     53  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     54  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     55  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     56  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     57  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     58  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     59  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     60  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     61  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     62  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     63  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     64  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     65  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     66  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     67  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     68  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     69  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     70  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     71  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     72  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     73  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     74  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     75  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     76  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     77  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     78  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     79  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     80  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     81  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     82  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     83  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     84  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     85  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     86  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     87  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     88  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     89  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     90  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     91  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     92  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     93  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     94  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     95  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     96  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     97  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     98  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM     99  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    100  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    101  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    102  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    103  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    104  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    105  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    106  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    107  Ar                  0.000   0.000   0.000  1.00  1.00
ATOM    108  Ar                  0.000   0.000   0.000  1.00 10.00

In this chages masses are read from the occupancy column and charges are read from the beta column.

Using this command to read in masses and charges is useful when you are postprocessing a trajectory using driver. If you are using PLUMED as a plugin to a molecular dynamics code the masses and charges will often be passed from the MD code to PLUMED.

Syntax

The following table describes the keywords and options that can be used with this action

Keyword Type Default Description
PDBFILE compulsory none a pdb file that contains the masses and charges of the atoms in the beta and occupancy columns
FILE optional not used input file that contains the masses and charges that should be used