VMD-L Mailing List

From: Jacob Graham (jacobgraham2025_at_u.northwestern.edu)
Date: Tue Jun 18 2024 - 14:59:45 CDT

I think there is a bug when using the -skip parameter of namdenergy from
the command line.

I am using VMD for LINUXAMD64, version 1.9.3 (November 30, 2016) and the
NAMD Energy Plugin, Version 1.4 to calculate energies between 2 molecules
throughout a .dcd format trajectory. Instead of calculating the energy for
every frame in my trajectory, I am trying to calculate it for every 10th
frame. In order to do this, I am passing '-skip 9' to the namdenergy
command. However, in the output file I noticed that the frame number and
time reported in the first two columns were going higher than the number of
frames and time in the trajectory. When I reran the energy calculations
passing '-skip 0' to the namdenergy command, this problem went away. When
comparing the two output files, I noticed that values reported as frame 10,
while using -skip 9 corresponded to the same values reported as frame 9
while using -skip 0. Values reported as frame 20 while using -skip 9
corresponded to the same values reported as frame 18 while using -skip 0.

By my understanding, -skip n should skip n frames and calculate energy for
every (n+1)th frame as it is explained in the documentation (
https://www.ks.uiuc.edu/Research/vmd/plugins/namdenergy/). It appears to
instead be calculating energy every (n+1)th frame, but reporting that those
values are for the nth frame when using -skip.

Here is an example of the output from namdenergy while passing -skip 9:

Frame Time Elec VdW Nonbond Total

0 0 -21.9162 -0.9314 -22.8476
 -22.8476
10 250000 -29.1755 -12.2471 -41.4226
 -41.4226
20 500000 -45.4165 -17.1429 -62.5594
 -62.5594
30 750000 -46.1839 -17.1731 -63.357
-63.357

Here is an example of the output from namdenergy while passing -skip 0:

Frame Time Elec VdW Nonbond Total

0 0 -21.9162 -0.9314 -22.8476
 -22.8476
1 25000 -25.1932 -3.7803 -28.9735
 -28.9735
2 50000 -24.2 -2.3902 -26.5902
 -26.5902
3 75000 -16.2648 -6.8729 -23.1377
 -23.1377
4 100000 -76.8927 -10.6238 -87.5165
 -87.5165
5 125000 -40.3515 -9.2048 -49.5563
 -49.5563
6 150000 -57.7284 -10.5919 -68.3203
 -68.3203
7 175000 -85.7217 -9.7696 -95.4913
 -95.4913
8 200000 -31.3831 -11.8777 -43.2608
 -43.2608
9 225000 -29.1755 -12.2471 -41.4226
 -41.4226
10 250000 -15.114 -12.7385 -27.8525
 -27.8525
11 275000 -78.0499 -16.191 -94.2409
 -94.2409
12 300000 -55.0642 -16.8925 -71.9567
 -71.9567
13 325000 -61.9645 -13.9181 -75.8826
 -75.8826
14 350000 -36.7297 -22.0884 -58.8181
 -58.8181
15 375000 -54.2946 -10.5093 -64.8039
 -64.8039
16 400000 -51.3829 -14.1861 -65.569
-65.569
17 425000 -19.3285 -19.999 -39.3275
 -39.3275
18 450000 -45.4165 -17.1429 -62.5594
 -62.5594
19 475000 -39.6884 -18.2573 -57.9457
 -57.9457
20 500000 -27.6637 -23.3253 -50.989
-50.989
21 525000 -39.3987 -23.0473 -62.446
-62.446
22 550000 -32.7096 -20.5993 -53.3089
 -53.3089
23 575000 -51.2034 -19.2007 -70.4041
 -70.4041
24 600000 -46.6593 -20.738 -67.3973
 -67.3973
25 625000 -38.3873 -15.928 -54.3153
 -54.3153
26 650000 -33.5287 -16.0382 -49.5669
 -49.5669
27 675000 -46.1839 -17.1731 -63.357
-63.357

I confirmed that this means -skip 0 and -skip 1 will both calculate
energies at each frame, but -skip 1 will double each Frame number and Time.

Here is an example of the output from namdenergy while passing -skip 1:

Frame Time Elec VdW Nonbond Total

0 0 -21.9162 -0.9314 -22.8476
 -22.8476
2 50000 -25.1932 -3.7803 -28.9735
 -28.9735
4 100000 -24.2 -2.3902 -26.5902
 -26.5902
6 150000 -16.2648 -6.8729 -23.1377
 -23.1377
8 200000 -76.8927 -10.6238 -87.5165
 -87.5165
10 250000 -40.3515 -9.2048 -49.5563
 -49.5563
12 300000 -57.7284 -10.5919 -68.3203
 -68.3203
14 350000 -85.7217 -9.7696 -95.4913
 -95.4913
16 400000 -31.3831 -11.8777 -43.2608
 -43.2608
18 450000 -29.1755 -12.2471 -41.4226
 -41.4226
20 500000 -15.114 -12.7385 -27.8525
 -27.8525
22 550000 -78.0499 -16.191 -94.2409
 -94.2409
24 600000 -55.0642 -16.8925 -71.9567
 -71.9567
26 650000 -61.9645 -13.9181 -75.8826
 -75.8826
28 700000 -36.7297 -22.0884 -58.8181
 -58.8181
30 750000 -54.2946 -10.5093 -64.8039
 -64.8039
32 800000 -51.3829 -14.1861 -65.569
-65.569
34 850000 -19.3285 -19.999 -39.3275
 -39.3275
36 900000 -45.4165 -17.1429 -62.5594
 -62.5594
38 950000 -39.6884 -18.2573 -57.9457
 -57.9457
40 1000000 -27.6637 -23.3253 -50.989
-50.989
42 1050000 -39.3987 -23.0473 -62.446
-62.446
44 1100000 -32.7096 -20.5993 -53.3089
 -53.3089
46 1150000 -51.2034 -19.2007 -70.4041
 -70.4041
48 1200000 -46.6593 -20.738 -67.3973
 -67.3973
50 1250000 -38.3873 -15.928 -54.3153
 -54.3153
52 1300000 -33.5287 -16.0382 -49.5669
 -49.5669
54 1350000 -46.1839 -17.1731 -63.357
-63.357

Please confirm if you think my logic is sound.

Best,

Jacob