AMBER Archive (2009)

Subject: Re: Re: [AMBER] error in distance restraint

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Thu Oct 29 2009 - 05:20:13 CDT

the energy is zero, not the distance. if there is no deviation, there is no
penalty (as Adrian Roitberg pointed out).
the important thing is to analyze your structures and see if the distance
stays in the range you requested.

2009/10/28 xuemeiwang1103 <xuemeiwang1103_at_163.com>

> Dear Dr.Carlos:
> Thanks a lot for your suggestion.Pardon me for not having a full
> comprehend of the NMR distance restriant ,Doesn't it seem strange that the
> NMR disctance restriant is 0.00 after 250 steps ? NMR restraints: Bond =
> 0.000 Angle = 0.000 Torsion = 0.000
>
>
>
>
>
>
> 在2009-10-29，"Carlos Simmerling" <carlos.simmerling_at_gmail.com> 写道：
> >why do you say it failed? did you measure the distance and find that it
> >moved outside the restraint region?
> >
> >2009/10/28 xuemeiwang1103 <xuemeiwang1103_at_163.com>
> >
> >>
> >>
> >>
> >> Dear Dr. :
> >>
> >> Thanks a lot for your detailed explanation and several useful
> suggestions
> >> .I tried it again ,I found the computer can calculated if I removed
> ntr=1
> >> and just keep nmropt=1 in my input file,but the strange things happened
> >> again,the NMR restraint seems just took effect in the first few steps
> ,cound
> >> you tell me where I went wrong in my input,I really felt very bad about
> >> this problem ,thank you very much!
> >>
> >> my input:
> >>
> >> Stage 1 heating of 1o86 0 to 50K
> >>
> >> &cntrl
> >>
> >> imin=0,irest=0,ntx=1,
> >>
> >> nstlim=5000,dt=0.001,
> >>
> >> ntc=2,ntf=2,
> >>
> >> ntt=3,gamma_ln=1.0,
> >>
> >> tempi=0.0,temp0=50.0,
> >>
> >> ntb=1,cut=8,
> >>
> >> nmropt=1,
> >>
> >> ntpr=250,ntwx=500,ntwr=500,
> >>
> >> /
> >>
> >> &wt type='REST',istep1=0,istep2=5000,
> >>
> >> value1=1.0,value2=1.0,
> >>
> >> /
> >>
> >> &wt type='END' ,
> >>
> >> /
> >>
> >> LISTOUT=RST.out
> >>
> >> DISANG=dis.RST
> >>
> >> ---------------- dis.RST-----------
> >>
> >> #DISTANTENT.FILE
> >>
> >> &rst
> >>
> >> ixpk= 0, nxpk= 0, iat= 9292, 7786, r1= 1.20, r2= 1.50, r3= 2.00, r4=
> 5.00,
> >> rk2=10.0, rk3=10.0, ir6=1,
> >>
> >> /
> >>
> >> Outputfile :
> >>
> >> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS =
> >> 0.0
> >>
> >> Etot = -354165.8192 EKtot = 0.0000 EPtot =
> >> -354165.8192
> >>
> >> BOND = 323.2417 ANGLE = 1484.8635 DIHED =
> >> 2630.5202
> >>
> >> 1-4 NB = 1853.1531 1-4 EEL = 23829.9363 VDWAALS =
> >> 62903.2679
> >>
> >> EELEC = -447237.1261 EHBOND = 0.0000 RESTRAINT =
> >> 46.3241
> >>
> >> EAMBER (non-restraint) = -354212.1433
> >>
> >> Ewald error estimate: 0.1509E-03
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >>
> >> NMR restraints: Bond = 46.324 Angle = 0.000 Torsion =
> 0.000
> >>
> >> NSTEP = 250 TIME(PS) = 0.250 TEMP(K) = 16.33 PRESS =
> >> 0.0
> >>
> >> Etot = -300871.8202 EKtot = 2700.2781 EPtot =
> >> -303572.0983
> >>
> >> BOND = 374.7332 ANGLE = 1603.3394 DIHED =
> >> 2663.7262
> >>
> >> 1-4 NB = 1865.1801 1-4 EEL = 23834.0649 VDWAALS =
> >> 46987.7396
> >>
> >> EELEC = -380900.8816 EHBOND = 0.0000 RESTRAINT =
> >> 0.0000
> >>
> >> Ewald error estimate: 0.3079E-03
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >>
> >> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> 0.000
> >>
> >> NSTEP = 500 TIME(PS) = 0.500 TEMP(K) = 25.26 PRESS =
> >> 0.0
> >>
> >> Etot = -298494.3179 EKtot = 4176.6006 EPtot =
> >> -302670.9184
> >>
> >> BOND = 408.2542 ANGLE = 1694.0090 DIHED =
> >> 2691.5324
> >>
> >> 1-4 NB = 1886.3935 1-4 EEL = 23852.1110 VDWAALS =
> >> 48006.3952
> >>
> >> EELEC = -381209.6138 EHBOND = 0.0000 RESTRAINT =
> >> 0.0000
> >>
> >> Ewald error estimate: 0.2284E-03
> >>
> >>
> >>
> ------------------------------------------------------------------------------
> >>
> >> NMR restraints: Bond = 0.000 Angle = 0.000 Torsion =
> 0.000
> >>
> >>
> >>
> ===============================================================================
> >>
> >>
> >>
> >>
> >>
> >>
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> >>
> >>
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