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.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
>
>
-----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber.scripps.edu
> To unsubscribe, send "unsubscribe amber" to
> majordomo.scripps.edu
>
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://www.rosswalker.co.uk/adsense_alternatives/
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Wed Feb 23 2005 - 06:53:01 PST
