RMS of ~10 kcal/mol is not un-reasonable. RMS is different from error bar. ... in addition, different molecular systems have different RMS. Hope this help. Best. Ying-chieh Sun
-----Original Message-----
From: 冉挺 [mailto:rantingjing0445019.gmail.com]
Sent: Saturday, November 9, 2013 1:10 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Erro in the Thermodynamic Intergration using soft core potentials"
Dear Prof. David,
I did first 100ps TI simulation,and its result is listed here. The "R M S F L U C T U A T I O N S" of DV/DL equal 10.2061, which seems much larger than the value given by the AMBER tutorial. So how could I make sure to get a smaller RMSD value of DV/DL.
_____________________________________
A V E R A G E S O V E R 100000 S T E P S
NSTEP = 100000 TIME(PS) = 420.000 TEMP(K) = 298.59 PRESS =
-86.4
Etot = -62471.6753 EKtot = 15873.3120 EPtot =
-78344.9873
BOND = 396.6721 ANGLE = 1089.8387 DIHED =
1377.5214
1-4 NB = 514.9656 1-4 EEL = 5341.4951 VDWAALS =
10136.1198
EELEC = -97287.4232 EHBOND = 0.0000 RESTRAINT =
85.8233
EAMBER (non-restraint) = -78430.8106
DV/DL = -8.0879
EKCMT = 7136.8883 VIRIAL = 7777.9838 VOLUME =
343956.0571
Density =
0.7742
Ewald error estimate: 0.7666E-04
------------------------------------------------------------------------------
Softcore part of the system: 3 atoms, TEMP(K) =
323.77
SC_Etot= 1.9302 SC_EKtot= 1.9302 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= 3.9292 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= -7.9723 SC_DERIV =
-7.9723
------------------------------------------------------------------------------
R M S F L U C T U A T I O N S
NSTEP = 100000 TIME(PS) = 420.000 TEMP(K) = 7.48 PRESS =
148.7
Etot = 936.6629 EKtot = 397.8939 EPtot =
628.6831
BOND = 18.5728 ANGLE = 41.4863 DIHED =
29.4301
1-4 NB = 10.7895 1-4 EEL = 31.2691 VDWAALS =
146.0418
EELEC = 353.7411 EHBOND = 0.0000 RESTRAINT =
443.3015
EAMBER (non-restraint) = 185.3816
DV/DL = 10.2061
EKCMT = 228.3245 VIRIAL = 1024.8504 VOLUME =
19338.7088
Density =
0.0433
Ewald error estimate: 0.5825E-04
------------------------------------------------------------------------------
Softcore part of the system: 3 atoms, TEMP(K) =
386.10
SC_Etot= 2.3018 SC_EKtot= 2.3018 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= 5.1688 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= 8.3297 SC_DERIV =
8.3297
------------------------------------------------------------------------------
My parameters are listed here.
For V0 state.
&cntrl
imin=0, irest=1, ntx=7, ibelly=0,
ntt=3, tempi=298.0,temp0=298.0, tautp=2.0, gamma_ln=2.0,
ntp=1, taup=2.0,ig=-1,nrespa=1,
ntb=2, ntc=2, ntf=1,
cut=12.0, nsnb=20,dt=0.001,
nstlim=100000,ntr=1,
ntwe=500, ntwx=500, ntpr=50,
icfe=1, clambda=0.2,
ifsc=1,
crgmask=':136.O,H1,H2', scmask=':136.O,H1,H2', &end Title five
2.01
RES 136
END
END
the V1 state had the same parameters as the v0 state.
On Friday, October 4, 2013, David A Case wrote:
> On Thu, Oct 03, 2013, 冉挺 wrote:
> >
> > In my mind, I use the miniminzed structure to produce V0.top and
> > V1.top and then run TI simulation respectively, is that right? or
> > should
> I
> > use the two unminimized structure V0.top and V1.top to minimized
> > first respectively and then run TI simulation respectively.
> >
> > In addition, I suppose TI simulation should be run after the
> > molecular system has been heated and reachs the equlibrium state, so
> > if all lamda window TI simulations can be carried out based on the
> > same equilibrated
> rst
> > file?
>
> TI runs on a mixed potential energy surface, but otherwise
> equilibration takes place as normal. It is not quite clear (to me!)
> what you are asking here.
>
> As the code tells you, you *must* have *exactly* the same coordinates
> for the common atoms in V0 and V1. You cannot (for example) minimize
> one structure in the V0 force field, and the other in the V1 force
> field, then use those as starting points.
>
> For your second question: you need to equilibrate the system anew for
> every value of lambda. You cannot use a single "equilibrated rst
> file" for all lambda values. The force field is different for each
> lambda, and hence the equilibration must be re-done.
>
> ...hope this helps...dac
>
>
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>
--
PhD Ting Ran
CPU(CHINA PHARMACEUTICAL UNIVERSITY)
Molecular-Design & Drug-Discovery Lab
Laboratory Building A212
639 Longmian Avenue
Nanjing, 210009
P.R.China
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Received on Sun Nov 10 2013 - 00:00:02 PST
