there are really two issues here:
1) not having restraints in step 2. I think you should diff the input files
and make sure the only differences are the ones you want. the IISTIN might
me a problem in step 2, try fixing that.
2) you are NOT doing what the community would consider "heating". you are
assigning initial velocities at 1 temperature (tempi) and immediately
setting the thermostat to a higher temperature. especially with ntt=3, this
system temperature will reach temp0 very quickly. so this is not what would
be considered "heating" in the sense of gradual heating during and
equilibration. certainly if you said in a paper that you heated the system
over the course of this run it would not be correct. check the temperature
of the system as reported in the mdout file- it will not be gradual heating.
to do that, you need to slowly change the thermostat itself (temp0) in the
weight change section of your restraints (%wt).
2010/5/5 xuemeiwang1103 <xuemeiwang1103.163.com>
> Dear all:
> I want to constraint the distance between four atoms(GLU355 OE1-WAT588
> H1,GLU355 OE2-WAT637 H1),so I use the NMR restraint in my mdin file , After
> minimal the system,I began to heat it to 300K over 6 stages.The strange
> thing is that the NMR restraint seems only work at first two stages ,when
> the Tem reach to 300K,the distance is still far.Could someone tell me the
> reason? Thank you !
>
>
> My input file:
>
> Stage 1 heating 50 to 100K
>
> &cntrl
>
> imin=0,irest=1,ntx=5,
>
> nstlim=5000,dt=0.001,
>
> ntc=2,ntf=2,
>
> ntt=3,gamma_ln=1.0,
>
> tempi=50.0,temp0=100.0,
>
> ntb=1,cut=8,
>
> nmropt=1,
>
> ntpr=250,ntwx=500,ntwr=500,
>
> /
>
> &wt type='END' ,
>
> /
>
> LISTIN=POUT
>
> LISTOUT=RST.out
>
> DISANG=dis.RST
>
> The dis.RST
>
> #DISTANTENT.FILE
>
> &rst
>
> ixpk= 0, nxpk= 0, iat= 9299, 5551, r1= 0.84, r2= 1.34, r3= 2.34, r4= 2.84,
> rk2= 25.0, rk3= 25.0, ir6=1,ialtd= 0,
>
> /
>
> &rst
>
> iat= 69425, 5550, r1= 0.84,r2= 1.34, r3= 2.34, r4=2.84,rk2= 25.0,rk3=
> 25.0,
>
> /
>
> Outputfile:
>
> 3. ATOMIC COORDINATES AND VELOCITIES
>
>
> -------------------------------------------------------------------------------
>
> begin time read from input coords = 5.000 ps
>
> Begin reading energy term weight changes/NMR restraints
>
> WEIGHT CHANGES:
>
> ** No weight changes given **
>
> RESTRAINTS:
>
> Requested file redirections:
>
> LISTIN = POUT
>
> LISTOUT = RST.out
>
> DISANG = dis.RST
>
> Restraints will be read from file: dis.RST
>
> Here are comments from the DISANG input file:
>
> #DISTANTENT.FILE
>
> ******
>
> H1 ( 9299)-OE2 ( 5551) NSTEP1= 0 NSTEP2=
> 0
>
> R1 = 0.840 R2 = 1.340 R3 = 2.340 R4 = 2.840 RK2 = 25.000 RK3 =
> 25.000
>
> Rcurr: 2.272 Rcurr-(R2+R3)/2: 0.432 MIN(Rcurr-R2,Rcurr-R3):
> 0.000
>
> ******
>
> H1 (69425)-OE1 ( 5550) NSTEP1= 0 NSTEP2=
> 0
>
> R1 = 0.840 R2 = 1.340 R3 = 2.340 R4 = 2.840 RK2 = 25.000 RK3 =
> 25.000
>
> Rcurr: 2.123 Rcurr-(R2+R3)/2: 0.283 MIN(Rcurr-R2,Rcurr-R3):
> 0.000
>
> Number of restraints read = 2
>
> Done reading weight changes/NMR restraints
>
> Input file:
>
> Stage 1 heating 150 to 200K
>
> &cntrl
>
> imin=0,irest=1,ntx=5,
>
> nstlim=5000,dt=0.001,
>
> ntc=2,ntf=2,
>
> ntt=3,gamma_ln=1.0,
>
> tempi=150.0,temp0=200.0,
>
> ntb=1,cut=8,
>
> nmropt=1,
>
> ntpr=250,ntwx=500,ntwr=500,
>
> /
>
> &wt type='END' ,
>
> /
>
> lISTIN=POUT
>
> LISTOUT=RST.out
>
> DISANG=dis.RST
>
> Outputfile:
>
> 3. ATOMIC COORDINATES AND VELOCITIES
>
>
> -------------------------------------------------------------------------------
>
> begin time read from input coords = 10.000 ps
>
> Begin reading energy term weight changes/NMR restraints
>
> WEIGHT CHANGES:
>
> ** No weight changes given **
>
> RESTRAINTS:
>
> No valid redirection requests found
>
> ** No restraint defined **
>
> Done reading weight changes/NMR restraints
>
>
>
>
>
>
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Received on Wed May 05 2010 - 04:30:04 PDT
