# [AMBER] problems with FEP calculations

From: Małgorzata Kogut <malgorzata.kogut.phdstud.ug.edu.pl>
Date: Mon, 22 Nov 2021 14:45:25 +0000

Hi there,

I tried to perform FEP calculations based on the tutorial https://ambermd.org/tutorials/advanced/tutorial9/index.html#run_TI.
During the TI simulation (for pmemd} that was divided for 101 windows (with lambda value between 0.00 - 1.00 with 0,01 step) we observed that for some frames values for DV/DL did not appear in the output. My question would be why such an event would occur and if there is anything that can be done to have the full record of DV/DL in each window.

Below, the examples from a chosen window for frames where DV/DL was not and was recorded:

| TI region 1

NSTEP = 98000 TIME(PS) = 198.000 TEMP(K) = 291.45 PRESS = 7.6
Etot = -2779.8929 EKtot = 683.6971 EPtot = -3463.5901
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 595.7404
EELEC = -4059.3304 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 341.5981 VIRIAL = 288.2785 VOLUME = 323710.2458
Density = 0.0376
Ewald error estimate: 0.6751E-04
------------------------------------------------------------------------------

Softcore part of the system: 1 atoms, TEMP(K) = 487.69
SC_Etot= 1.4537 SC_EKtot= 1.4537 SC_EPtot = 0.0000
SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000
SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000
SC_EEL = 0.0000
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 0.0000 SC_VDW_DER= 0.0000 SC_DERIV = 0.0000
------------------------------------------------------------------------------

| TI region 2

NSTEP = 98000 TIME(PS) = 198.000 TEMP(K) = 291.59 PRESS = 7.6
Etot = -2779.5484 EKtot = 684.0416 EPtot = -3463.5901
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 595.7404
EELEC = -4059.3304 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 341.5981 VIRIAL = 288.2785 VOLUME = 323710.2458
Density = 0.0376
Ewald error estimate: 0.6751E-04
------------------------------------------------------------------------------

TI region 1

NSTEP = 99000 TIME(PS) = 200.000 TEMP(K) = 302.80 PRESS = -11.7
Etot = -2729.9491 EKtot = 710.3337 EPtot = -3440.2828
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 568.2208
EELEC = -4008.5036 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 348.5883 VIRIAL = 430.6263 VOLUME = 323674.4292
Density = 0.0376
DV/DL = -0.0265
Ewald error estimate: 0.2092E-04
------------------------------------------------------------------------------

Softcore part of the system: 1 atoms, TEMP(K) = 320.86
SC_Etot= 0.9564 SC_EKtot= 0.9564 SC_EPtot = 0.0000
SC_BOND= 0.0000 SC_ANGLE= 0.0000 SC_DIHED = 0.0000
SC_14NB= 0.0000 SC_14EEL= 0.0000 SC_VDW = 0.0000
SC_EEL = 0.0000
SC_RES_DIST= 0.0000 SC_RES_ANG= 0.0000 SC_RES_TORS= 0.0000
SC_EEL_DER= 0.0000 SC_VDW_DER= -0.0001 SC_DERIV = -0.0001
------------------------------------------------------------------------------

| TI region 2

NSTEP = 99000 TIME(PS) = 200.000 TEMP(K) = 303.09 PRESS = -11.7
Etot = -2729.2810 EKtot = 711.0018 EPtot = -3440.2828
BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 568.2208
EELEC = -4008.5036 EHBOND = 0.0000 RESTRAINT = 0.0000
EKCMT = 348.5883 VIRIAL = 430.6263 VOLUME = 323674.4292
Density = 0.0376
DV/DL = -0.0265
Ewald error estimate: 0.2092E-04
------------------------------------------------------------------------------

Cheers,

Małgosia

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Received on Mon Nov 22 2021 - 07:00:03 PST
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