output

Outputs from erdst run

engsln.XX

engsln.XX is an output only in a soln run.
This output file is an input to the slvfe program to compute the solvation free energy.
As of version 1.0 ,engsln.XX typically reads like

...
  -4.370000      -4.345000        1    0.350465725129100E-01    0.700931450258191
  -4.320000      -4.295000        1    0.380929927424355E-01    0.761859854848727
  -4.270000      -4.245000        1    0.339955644632201E-01    0.679911289264393
  -4.220000      -4.195000        1    0.429572985100842E-01    0.859145970201672
  -4.170000      -4.145000        1    0.300335490894311E-01    0.600670981788636
...

The first and second columns in each line correspond to the discretized, pair energy between solute and solvent.
The first column refers to the beginning of the energy bin (smallest energy of the bin).
The second column is the middle point of the energy bin. To be more precise, it is the middle of the end energies of the bin when the energy is smaller than eccore described in Parameter files for erdst and is the geometric mean of the end values when the energy is larger than eccore. The end values are the values in the first columns in the same and next lines.
The third column in each line identifies the solvent species. When its value is 2, for example, the line refers to the pair energy between the solute and the 2nd solvent species. Even when the solvent is not a mixed one and the number of solvent species is unity, the third column is present and is equal to 1.
The fourth column is the averaged histogram, the average number of solvent molecules which belong to the species identified by the third column and have the pair energy within the bin specified by the first and second columns. Since the fourth column is the average histogram, it is summed over all the meshes of energy to provide the total number of solvent molecules.
The fifth column is the density (i.e. the value in the fourth column / bin width).

On Version 0.3 or below, the format is:

...
  -4.345000        1    0.350062612200486E-01
  -4.295000        1    0.449868172583639E-01
  -4.245000        1    0.430109979475901E-01
  -4.195000        1    0.341330443566083E-01
  -4.145000        1    0.339685912443535E-01
...

The first, second, and third columns correspond to the second, third, and fourth columns in the above, respectively.
It should be noted that the third column is the average histogram, not the density. To determine the pair-energy density, the value at the third column needs to be divided by the width of the corresponding mesh.

engref.XX and corref.XX

engref.XX and corref.XX are outputs only in a refs run.
They are inputs to the slvfe program to compute the solvation free energy.

The format of engref.XX is the same as that of engsln.XX described above.
It provides the averaged histogram of pair energy when the solute is inserted into the reference solvent as a test particle.

corref.XX is given as a binary file.
It stores the two-body histogram, which becomes the variance or covariance when the product of the one-body histograms in the corresponding engref.XX is subtracted.
The subtraction is done in the slvfe program, and ermod outputs only the two-body histogram as corref.XX.

aveuv.tt

aveuv.tt is an output only in a soln run.
It provides the average sum of the solute-solvent interaction energy in each block of the MD trajectory in soln.
As described in Parameter files for erdst, the MD trajectory in soln is divided in into a certain number of blocks specified by engdiv, and the average sum is given for each block.
Typically, aveuv.tt reads like

    1      -20.68111
    2      -22.01607
...
    8      -20.82699
    9      -21.68679
   10      -19.84933

In this example, the number of solvent species is unity.
In each line, the first column refers to the block number and the subsequent column lists the average sum of the solute-solvent interaction energy.
In the example given above, the number of blocks is 10 (engdiv = 10).
The first line gives the average sum of the solute-solvent interaction energy in the 1st block.
The second line is for the average energy in the 2nd block, and so on.

When the solvent is a mixed one and the number of solvent species is 2 or more, aveuv.tt looks like

    1      -4.50374      -13.55533
    2      -5.24531      -11.34801
...

The second column is the average sum of the interaction energy of the solute with the 1st solvent species, and the third column is the average energy with the 2nd solvent species.
The second and subsequent columns report the average interaction energies of the solute with the 1st, 2nd, and ... solvent species.

See also Notes on the outputs of slvfe for mixed solvent at the end of the Running slvfe: Getting Final Output sectin of Quick Start Guide for the output convention for aveuv.tt

See Finite concentration of solute: when more than one molecules are present for the solute species when more than one molecules are present for the solute species.
Suppose, for example, that the soln system consists of 100 EtOH molecules and some water molecules.
When EtOH is the solute, one of the 100 EtOH molecules is actually treated as the 'solute' and the other 99 are treated as part of the mixed solvent; the mixed solvent consists of 99 EtOH molecules and the water molecules.
For a single snapshot of the soln trajectory, ermod performs 100 samplings of solute-solvent configuration.
In the 1st sampling, the 1st EtOH molecule is treated as the solute, and the solute-solvent interactions of the solute EtOH are calculated against the 99 'solvent' molecules of the 2nd to 100th EtOH molecules as well as against all the water molecules.
In the 2nd sampling, the 2nd EtOH molecule is treated as the solute, and the solute-solvent interactions of the solute EtOH are calculated against the 99 'solvent' molecules of the 1st and the 3rd to 100th EtOH molecules as well as against the water molecules.
And the 3rd to 100th EtOH molecules are treated similarly.
aveuv.tt then provides two energy values; one is for the average sum of the interaction energy of the ‘solute’ EtOH molecule and the ‘solvent’ EtOH molecules, and the other represents the average sum of the interaction energy of the ‘solute’ EtOH molecule and the water molecules.
Actually, the average energy is the one also averaged over the 100 EtOH molecules which are treated as the ‘solute’ in turn.
Thus, the average energy for the ‘solute’ EtOH molecule and the ‘solvent’ EtOH molecules is the average sum of the interaction energy of 1 EtOH molecule and the other 99 EtOH molecules, and the average energy for the ‘solute’ EtOH molecule and the ‘solvent’ water is the average sum of the interaction energy of a single EtOH molecule and all the water molecules.

uvrange.tt

uvrange.tt is an output both in soln and refs runs, and provides the minimum and maximum values of the interaction energy of the solute with each solvent species.
This file is generated when the erdst program finishes successfully.
A uvrange.tt output looks like

 species     minimum        maximum
    0       -0.08086        0.00799
    1      -30.66799       14.66573
    2       -7.40580        5.36599
...

In this list, the species 0 corresponds to the self-enegy of the solute.
Shown are the minimum and maximum of the solute self-energy.
The self-energy is usually small in magnitude when a large MD unit cell is used.
The species 1 is the 1st solvent species,
and the minimum and maximum of the pair energy between the solute and the 1st solvent species are shown.
Similarly for the species 2, and so on.
In this example, the minimum pair energy of the solute is -30.7 kcal/mol against the solvent species 1 and is -7.4 kcal/mol against the solvent species 2.

The above example is for the solution system (soln).
When the system is the reference solvent (refs), the value of the maximum energy will be very large.
The solute is inserted into the reference solvent as a test particle, and the overlap of solute and solvent is allowed.
The pair energy is very large at overlap, and this is reflected in a large maximum observed in uvrange.tt of reference solvent.

weight_soln and weight_refs

weight_soln is an output in a soln run and weight_refs is an output in a refs run.
They give the statistical weight for each block of the MD trajectory; the number of blocks is specified by engdiv described in Parameter files for erdst.
When some average is to be taken over the blocks, the weights provided in weight_soln or weight_refs are assigned to the blocks.

There are two formats of output depending on the value of wgtslf described in Parameter files for erdst.
When wgtslf = 0 (default setting in a soln calculation and in a refs calculation without the Ewald or PME method), the typical output looks like

    1      0.10000000E+01
    2      0.10000000E+01
    3      0.10000000E+01
...

in the case of NVT ensemble and is like

    1      0.14825020E+05
    2      0.14906728E+05
    3      0.14996490E+05
...

in the case of NPT ensemble.

In each line, the first column refers to the block number and the second column is the weight.
The weight is not normalized, and when the NPT ensemble is adopted, the weight stored is often close to the average volume of the system in the trajectory block.
Note that since the weight is often modified with a system-dependent and/or solute-dependent factor, it may not be exactly equal to the average volume.

When wgtslf = 1 (default setting in a refs calculation with the Ewald or PME method), the typical output reads like

    1      0.14752840E+05      -0.1201259E-01
    2      0.14852257E+05      -0.1192963E-01
    3      0.14839418E+05      -0.1195628E-01
...

The first and second columns have the same meanings as above.
The third line is the self-energy of the solute averaged within the block; see (2) Self-Energy of the Solute within Running slvfe: Getting Final Output section of Quick Start Guide.

flcuv.tt

flcuv.tt is an output only in a soln run.
It lists the sum of the solute-solvent interaction energy at each MD snapshot.
The progress of a soln run can also be seen from flcuv.tt.

When the solvent is not a mixed one and the number of solvent species is unity, a typical output reads like

        1      -22.90690
        2      -23.19617
        3      -23.19417
...

In each line, the first column refers to the snapshot number of the solution MD, and the second column is the sum of the solute-solvent interaction energy at that snapshot.

When the solvent is a mixed one and the number of solvent species is 2 or more, flcuv.tt looks like

        1      -5.21563      -16.91873
        2      -4.78392      -18.09231
        3      -7.22345      -14.33231
...

when the solution system contains a single molecule for the solute species.
The first column is for the snapshot number.
The second column is the sum of the interaction energy of the solute with the 1st solvent species, and the third column is the average energy with the 2nd solvent species.
The second and subsequent columns report the sums of the interaction energies of the solute with the 1st, 2nd, and ... solvent species.

When more than one molecules are present for the solute species, the format is further modified into something like

        1        1       -0.55259      -17.04460
        2        1       -1.40880      -16.14232
...
        1        2       -0.26440      -17.54940
        2        2       -1.31680      -15.53015
...
        1        3       -0.00404      -18.01386
        2        3       -1.25651      -14.92891
...

In this case, the first column corresponds to the numbering of the solute.
For example, 1 means the 1st molecule of the solute species, 2 means the 2nd, and so on.
The second column is the snapshot number, and the third and subsequent columns report the sums of the interaction energies of the solute with the 1st, 2nd, and ... solvent species.

See also Notes on the outputs of slvfe for mixed solvent at the end of the Running slvfe: Getting Final Output sectin of Quick Start Guide for the output convention for flcuv.tt

See also the description for aveuv.tt given above and Finite concentration of solute: when more than one molecules are present for the solute species.
When the system contains more than one molecules for the solute species, the system is always treated as a mixed solvent by viewing, in turn, one of the solute molecules as 'solute' and the others as 'solvent'.

progress.tt

progress.tt is an output only in a refs run.
This output provides the number of the reference-solvent snapshot for which the test-particle insertions and the accompanying energy calculations are done.
It looks like

           1           2           3           4
           5           6           7           8
           9          10          11          12
          13          14          15          16
...

Each value shows the snapshot number.
progress.tt is generated only to see the progress of a refs run, and contains no physical or chemical information.