AMBER Archive (2009)

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

From: xuemeiwang1103 (xuemeiwang1103_at_163.com)
Date: Wed Oct 28 2009 - 22:43:55 CDT

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

ÔÚ2009-10-29£¬"Carlos Simmerling" <carlos.simmerling_at_gmail.com> дµÀ£º
>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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