AMBER Archive (2009)

Subject: Re: [AMBER] error in distance restraint

From: Adrian Roitberg (roitberg_at_qtp.ufl.edu)
Date: Wed Oct 28 2009 - 09:01:07 CDT

This is exactly the right behavior
It is not that the restraint is not working, but rather that is working
perfectly. You told the system to try to put the distance
between atoms 9292 and 7786 between 1.5 and 2 Angstroms. The system
tried it, and succeded, at which point the
Restraint energy is zero, because you are in flat section of your
potential restraint.

Adrian

xuemeiwang1103 wrote:
>
>
> 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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-- 
                            Dr. Adrian E. Roitberg
                              Associate Professor
                             Quantum Theory Project
                            Department of Chemistry

                  Senior Editor. Journal of Physical Chemistry
                           American Chemical Society

University of Florida                         PHONE 352 392-6972
P.O. Box 118435                               FAX   352 392-8722
Gainesville, FL 32611-8435                    Email adrian_at_qtp.ufl.edu

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