Dear Amber users and developers,
I would like to share two different mdout and mdin for my thermodynamic integration run at lambda = 0.00922 and lambda = 0.999. This was done for van der Waals removal stage in the two-step absolute binding free energy calculation. I have used softcore for the ligand mask with charge zero at the start of the simulation. In both the mdouts it can be seen that
VDWAALS energy is the same for both the TI regions 1 and 2. This similarity can be seen for DV/DL as well. However, the total energy differs only with total kinetic energy here. I was under the impression with the removal of vdW from the ligand VDWAALS energy contribution for TI region 2 should decrease. Also, the temperature for the softcore part of the system is 50 K higher than the system temperature. This could be the reason for high kinetic energy. Still, I'm not sure why the temperature is different. These trends are similar under both the lambda values. I have simulated these systems over 25 ns and the trend is the same. I appreciate any valid explanation for this kind of scenario. It would allow me to validate if I'm following a correct approach to my calculation. Here's an extract from the file mdout0.999
| TI region 1
NSTEP = 500000 TIME(PS) = 1038150.000 TEMP(K) = 297.68 PRESS = 0.0
Etot = -109139.2433 EKtot = 37813.9058 EPtot = -146953.1491
BOND = 26459.0804 ANGLE = 398.1468 DIHED = 705.4525
1-4 NB = 190.2757 1-4 EEL = -2245.6457 VDWAALS = 28452.5254
EELEC = -201064.6956 EHBOND = 0.0000 RESTRAINT = 151.7113
EAMBER (non-restraint) = -147104.8605
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 412434.9426
Density = 1.0538
DV/DL = 35.9966
Ewald error estimate: 0.1369E-04
------------------------------------------------------------------------------
Softcore part of the system: 90 atoms, TEMP(K) = 332.25
SC_Etot= 280.2924 SC_EKtot= 89.1342 SC_EPtot = 191.1582
SC_BOND= 37.3510 SC_ANGLE= 87.4837 SC_DIHED = 51.3074
SC_14NB= 20.1244 SC_14EEL= 0.0000 SC_VDW = -5.1082
SC_EEL = 0.0000
SC_RES_DIST= 12.2855 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= -0.0000 SC_VDW_DER= -0.3876 SC_DERIV = -0.3876
------------------------------------------------------------------------------
| TI region 2
NSTEP = 500000 TIME(PS) = 1038150.000 TEMP(K) = 297.61 PRESS = 0.0
Etot = -109228.3775 EKtot = 37724.7716 EPtot = -146953.1491
BOND = 26459.0804 ANGLE = 398.1468 DIHED = 705.4525
1-4 NB = 190.2757 1-4 EEL = -2245.6457 VDWAALS = 28452.5254
EELEC = -201064.6956 EHBOND = 0.0000 RESTRAINT = 151.7113
EAMBER (non-restraint) = -147104.8605
EKCMT = 0.0000 VIRIAL = 0.0000 VOLUME = 412434.9426
Density = 1.0510
DV/DL = 35.9966
Ewald error estimate: 0.1369E-04
Thank you
Senal
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- application/octet-stream attachment: mdin0.999
Received on Thu Sep 09 2021 - 10:00:02 PDT
