Dear Amber,
After reading the Amber manual and a couple TI related publication, I
have a quite navy question: How can Amber calculate DV/DL during TI
calculation?
It looks to me that it is the summation of some energy terms of the
softcore part of the system, but not very sure which terms are included and
which are not.
Here is an example:
NSTEP = 250 TIME(PS) = 100.250 TEMP(K) =
301.06 PRESS = 223.5
Etot = -90941.2828 EKtot = 38415.3548 EPtot =
-129356.6376
BOND = 25991.2281 ANGLE = 2055.7814 DIHED =
4213.1786
1-4 NB = 930.7284 1-4 EEL = 12548.9046 VDWAALS =
24113.5279
EELEC = -199209.9866 EHBOND = 0.0000 RESTRAINT =
0.0000
*DV/DL = 10.6266*
EKCMT = 11611.7978 VIRIAL = 9618.8596 VOLUME =
412937.7546
Density =
1.0526
Ewald error estimate: 0.3218E-04
------------------------------------------------------------------------------
*Softcore part of the system: 1 atoms, TEMP(K) =
1534.78*
SC_Etot= 6.5438 SC_EKtot= 4.5748 SC_EPtot =
1.9689
SC_BOND= 1.5838 SC_ANGLE= 0.3042 SC_DIHED = 0.0536
SC_14NB= 0.0273 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_RES_PLPT= 0.0000 SC_RES_PLPL= 0.0000 SC_RES_GEN =
0.0000
SC_EEL_DER= 0.0000 SC_VDW_DER= 2.9867 SC_DERIV =
2.9867
------------------------------------------------------------------------------
Here are the energy terms of the other pair
NSTEP = 250 TIME(PS) = 100.250 TEMP(K) = 301.03 PRESS =
223.5
Etot = -90944.4775 EKtot = 38412.1601 EPtot =
-129356.6376
BOND = 25991.2281 ANGLE = 2055.7814 DIHED =
4213.1786
1-4 NB = 930.7284 1-4 EEL = 12548.9046 VDWAALS =
24113.5279
EELEC = -199209.9866 EHBOND = 0.0000 RESTRAINT =
0.0000
* DV/DL = 10.6266*
EKCMT = 11611.7978 VIRIAL = 9618.8596 VOLUME =
412937.7546
Density =
1.0527
Ewald error estimate: 0.3218E-04
------------------------------------------------------------------------------
* Softcore part of the system: 1 atoms, TEMP(K) =
464.06*
SC_Etot= 2.3169 SC_EKtot= 1.3833 SC_EPtot =
0.9336
SC_BOND= 0.1251 SC_ANGLE= 0.3212 SC_DIHED =
0.0536
SC_14NB= 0.4337 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_RES_PLPT= 0.0000 SC_RES_PLPL= 0.0000 SC_RES_GEN =
0.0000
SC_EEL_DER= 0.0000 SC_VDW_DER= 2.9867 SC_DERIV =
2.9867
------------------------------------------------------------------------------
The other question is that why DV/DL could fluctuate so wildly during the
simulation? In one of the TI tutorials, the instantaneous
DV/DL<
http://ambermd.org/tutorials/advanced/tutorial6/images/xmgrace3_large.jpg>fluctuate
significantly. I guess we can answer this question only after
knowing which terms are included in DV/DL. Please forgive any ignorance,
if any.
Cheers,
Henry
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Received on Mon Aug 12 2013 - 21:30:02 PDT
