AMBER Archive (2007)

Subject: Re: AMBER: Thermodynamic Integration with Explicit Solvent

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Wed Oct 10 2007 - 17:39:12 CDT

David and Thomas

I am trying this again following David's suggestions. Using the follow
group and input scripts (no shake this time) with serial and parallel (with
-ng 2) produced good results (see below)

-O -i ../TI-exe-water/mdTI.in.01 -p Octane.ES-TI.parm -c
../Octane.ES.md1.rst -o Octane.ES-TI.step01.out . . .
-O -i ../TI-exe-water/mdTI.in.01 -p 2-Octanone-Dummy.ES-TI.parm -c
2-Octanone-Dummy.ES-TI.eq3.rst -o 2-Octanone-Dummy.ES-TI.step01.out . . .

 &cntrl
   ntr=0,
   nstlim=3000000, nscm=2000, ntave=5000,
   ntx=7, irest=1, ntb=1, ntpr=100,
   ntp=0, taup=2.0,
   dt=0.001, nrespa=2,
   ntt=0, temp0 = 300., tautp= 2.0,
   ntc=1, ntf=1,
   ntwr = 10000, ntwx=0,
   cut=9.0,
 /

 NSTEP = 100 TIME(PS) = 13120.100 TEMP(K) = 238.47 PRESS =
0.0
 Etot = -12387.5794 EKtot = 3425.4284 EPtot = -
15813.0077
 BOND = 3406.0695 ANGLE = 7.6728 DIHED =
4.4646
 1-4 NB = 2.1128 1-4 EEL = -0.0882 VDWAALS =
2849.9746
 EELEC = -22083.2139 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.1731E-03
 ------------------------------------------------------------------------------
 . . . .
 NSTEP = 400 TIME(PS) = 13120.400 TEMP(K) = 255.37 PRESS =
0.0
 Etot = -12374.7257 EKtot = 3668.2543 EPtot = -
16042.9800
 BOND = 1713.4225 ANGLE = 8.0322 DIHED =
3.4233
 1-4 NB = 2.4275 1-4 EEL = -0.0886 VDWAALS =
3165.7025
 EELEC = -20935.8993 EHBOND = 0.0000 RESTRAINT =
0.0000
 Ewald error estimate: 0.8989E-04
 ------------------------------------------------------------------------------

We run into problems though when we added thermodynamic integration (icfe=1,
clambda = 0.00, klambda=6). The job terminated abnormally about 400 steps.
The regular energy values seem normal however the DV/DL problems are huge
despite clambda = 0.00.

 NSTEP = 100 TIME(PS) = 13120.100 TEMP(K) = 238.47 PRESS =
0.0
 Etot = -12387.5794 EKtot = 3425.4284 EPtot = -
15813.0077
 BOND = 3406.0695 ANGLE = 7.6728 DIHED =
4.4646
 1-4 NB = 2.1128 1-4 EEL = -0.0882 VDWAALS =
2849.9746
 EELEC = -22083.2139 EHBOND = 0.0000 RESTRAINT =
0.0000
 DV/DL = **************
 Ewald error estimate: 0.1731E-03
 ------------------------------------------------------------------------------
. . . .
NSTEP = 400 TIME(PS) = 13120.400 TEMP(K) = 255.37 PRESS =
0.0
 Etot = - 12374.7257 EKtot = 3668.2543 EPtot = -
16042.9800
 BOND = 1713.4225 ANGLE = 8.0322 DIHED =
3.4233
 1-4 NB = 2.4275 1-4 EEL = -0.0886 VDWAALS =
3165.7025
 EELEC = -20935.8993 EHBOND = 0.0000 RESTRAINT =
0.0000
 DV/DL = **************
 Ewald error estimate: 0.8989E-04
 ------------------------------------------------------------------------------

Any suggestions,

Thank you,

Scott

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