Hi,
I am performing a one-step Thermodynamic Integration (TI) calculation to
mutate Nd³⁺ into Yb³⁺ using non-softcore potentials. The calculations are
being run with *pmemd*, and I have set the keyword *logdvdl=1* so that all
dvdl values are printed at the end of the output file. However, in the
output file, I noticed that for certain values of lambda, I am getting the
following output:
"Summary of dvdl values over 3000000 steps:
-66.5444
-65.6382
-65.6035
-66.5655
-68.4412
-70.6788
-74.9736
-76.8827
-79.2861
-81.6753
-83 DV/DL = -75.6104
------------------------------------------------------------------------------
| TI region 2
NSTEP = 2971000 TIME(PS) = 9942.000 TEMP(K) = 301.27 PRESS =
-295.7
Etot = 701.5814 EKtot = 4726.2671 EPtot =
-4024.6857
BOND = 1221.1250 ANGLE = 5715.7708 DIHED =
254.9927
1-4 NB = 230.6009 1-4 EEL = -1597.6120 VDWAALS =
-4411.3206
EELEC = -5438.2425 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 249.6212 VIRIAL = 679.2109 VOLUME =
67280.8787
Density =
1.5612
DV/DL = -75.6104
------------------------------------------------------------------------------
wrapping first mol.: 0.00000 -41.36297 0.00000
| TI region 1
NSTEP = 2972000 TIME(PS) = 9944.000 TEMP(K) = 298.15 PRESS =
-226.7
Etot = 500.6744 EKtot = 4677.3059 EPtot =
-4176.6315
BOND = 1136.8646 ANGLE = 5669.4225 DIHED =
273.1395
1-4 NB = 232.1497 1-4 EEL = -1601.8612 VDWAALS =
-4442.9838
EELEC = -5443.3628 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 271.5141 VIRIAL = 600.0641 VOLUME =
67116.2837
Density =
1.5651
DV/DL = -84.0841
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 3000000 TIME(PS) = 10000.000 TEMP(K) = 3.41 PRESS =
218.4
Etot = 80.8584 EKtot = 53.5073 EPtot =
59.1317
BOND = 27.3286 ANGLE = 42.2949 DIHED =
16.2668
1-4 NB = 6.3059 1-4 EEL = 4.8573 VDWAALS =
29.6796
EELEC = 32.1384 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 12.6431 VIRIAL = 318.0937 VOLUME =
146.7919
Density =
0.0034
DV/DL = 8.3283
------------------------------------------------------------------------------
DV/DL, AVERAGES OVER 3000 STEPS
NSTEP = 3000000 TIME(PS) = 10000.000 TEMP(K) = 3.41 PRESS =
0.0
Etot = 0.0000 EKtot = 0.0000 EPtot =
-80.0102
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
-80.0102
EELEC = 0.0000 EHBOND = 0.0000 RESTRAINT =
0.0000
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME =
0.0000
Density =
0.0000
DV/DL = -80.0102
------------------------------------------------------------------------------
Summary of dvdl values over 3000000 steps:
-66.5444
-65.6382
-65.6035
-66.5655
-68.4412
-70.6788
-72.6413
-73.6938
-73.5737
-72.4873
-71.3136
-70.6830
-71.1013
-72.6630
-74.8109
-76.9463
-78.3785
-78.4292"
The output file initially prints 'Summary of dvdl values over 3,000,000
steps' and displays 1,664 steps. Then it proceeds with additional
calculations and later prints the complete 'Summary of dvdl values over
3,000,000 steps' with all the dvdl values included. I'm unsure why the
output is structured this way or what might be causing the issue. Any
insights or suggestions would be greatly appreciated.
Thank you.
Best,
Tamalika
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Received on Sun Sep 22 2024 - 12:30:02 PDT
