AMBER Archive (2005)

Subject: Re: AMBER: convert one functional group to another with TI

From: Eric Hu (yhu_2003_at_yahoo.com)
Date: Wed Feb 23 2005 - 00:36:03 CST

Ok, I perturbed one molecule to another which lacks by
a hydroxide only. I am thinking maybe I should
calculate the energy difference by perturbing both
molecules to nothing to prevent such big dV/dL values.
Anyway here are part of the lib, md.in and md.out
files:

####mol.lib####
!entry.ts1.unit.atoms table str name str type int
typex int resx int flags int seq int elmnt dbl
chg
 "C01" "CT" 0 1 131072 1 6 -0.114180
 "C02" "CT" 0 1 131072 2 6 0.321379
...
 "H43" "HP" 0 1 131072 43 1 0.0073370
 "H44" "H1" 0 1 131072 44 1 0.0143860
 "O45" "O" 0 1 131072 45 8 -1.097502
 "H46" "HO" 0 1 131072 46 1 0.3502950
!entry.ts1.unit.atomspertinfo table str pname str
ptype int ptypex int pelmnt dbl pchg
 "C01" "CT" 0 -1 0.152217
 "C02" "CT" 0 -1 -0.235196
...
 "H43" "HP" 0 -1 0.0510528
 "H44" "H1" 0 -1 -0.061306
 "O45" "DO" 0 -1 1.0975
 "H46" "DH" 0 -1 -0.350295
...
###md.in####
 neutralize toluene
&cntrl
 ntr=0,
 nstlim =1000000, 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=2, ntf=2, tol=0.000001,
 ntwr = 10000, ntwx=0,
 icfe=1, klambda=6, clambda=0.00922,
 cut=9.0,
/
###md.out###
...
------------------------------------------------------------------------------

      R M S F L U C T U A T I O N S

 NSTEP = 1000000 TIME(PS) = 1020.000 TEMP(K) =
   4.57 PRESS = 0.0
 Etot = 54.8570 EKtot = 35.6650
EPtot = 49.5257
 BOND = 2.4183 ANGLE = 3.4018
DIHED = 1.9551
 1-4 NB = 1.8223 1-4 EEL = 4.9543
VDWAALS = 53.7258
 EELEC = 81.8793 EHBOND = 0.0000
RESTRAINT = 0.0000
 DV/DL = 54.2857
|E(PBS) = 54.8472
 Ewald error estimate: 0.1275E-03

------------------------------------------------------------------------------
      DV/DL, AVERAGES OVER 500000 STEPS

 NSTEP = 1000000 TIME(PS) = 1020.000 TEMP(K) =
   0.00 PRESS = 0.0
 Etot = 0.0000 EKtot = 0.0000
EPtot = 1465.4880
 BOND = 0.0000 ANGLE = 0.0000
DIHED = 0.0000
 1-4 NB = 0.0000 1-4 EEL = 883.5451
VDWAALS = 0.0000
 EELEC = 581.9429 EHBOND = 0.0000
RESTRAINT = 0.0000
 Ewald error estimate: -0.1636E-04

------------------------------------------------------------------------------

--- "David A. Case" <case_at_scripps.edu> wrote:

> On Tue, Feb 22, 2005, Eric Hu wrote:
>
> > Does this seem suspicious to anyone too? Thanks.
>
> > Lamda DV/DL (in H2O)
> > 0.00922 1465.4880
>
> The above value looks suspicious to me, or at least
> like it will be hard
> to get precise averages when DV/DL is this big
> (check the standard deviation
> of this value over your trajectory). But without
> knowing more about what
> you did, I can't offer any real useful comments.
>
> ...dac
>
>
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