On Sat, Jun 02, 2007, D.Usharani wrote:
>
> 1. iresid=0 defining the distance restraint with atoms
> &rst
> ixpk =0, nxpk =0 iat = 3, 14,
> iresid=0,irstyp=1,ifvari=0,ninc=0,imult=1,ir6=0,ifntyp=0,
> ^^^^^^^^ *******
irstyp = 1 is very rarely used: I would not recommend it unless you are sure
you understand what it is doing.
>
> 2. Since the R1, R2, R3 and R4 values are not as given n the restraint i
> reseted irstyp=0 in the above input file.
>
> ####then out put is
> Begin reading energy term weight changes/NMR restraints
> WEIGHT CHANGES:
> DUMPFREQ 10 0 0.000000 0.000000 0 0
> ** No weight changes given **
> RESTRAINTS:
> Requested file redirections:
> LISTIN = POUT
> DISANG = distatom0.RST
> DUMPAVE = umbdistatom0.20
> Restraints will be read from file: distatom0.RST
> Here are comments from the DISANG input file:
>
> ******
> CA ( 3)-CA ( 14) NSTEP1= 0 NSTEP2=
> 0
> R1 = 0.000 R2 = 20.000 R3 = 20.000 R4 = 99.000 RK2 = 1.000 RK3 =
> 1.000
> Rcurr: 21.281 Rcurr-(R2+R3)/2: 1.281 MIN(Rcurr-R2,Rcurr-R3): 1.281
> Number of restraints read = 1
>
> Done reading weight changes/NMR restraints
> ###########
> So here R1-R4 values are as given in input file and DUMPAVE values are
> also 21.2- 19.77 .
Is this not what you want?
>
> In the two results it seems the restraint is like a well with square
> bottom parabolic sides.
This is correct, except that when r2 = r3 (as in your case) the width
of the "square bottom" is zero, so you just have a parbola.
> but I want to understand what does this Rcurr values signifies?
> what does the RESTRAINT printed at each step value signifies? and why
> does it decreases and becomes zero?
Rcurr is the current value of the distance. RESTRAINT is the restraint
energy; it decreases because md simulations tend to populate the regions of
lowest energy.
> ****
> EELEC = -6781.4141 EHBOND = 0.0000 RESTRAINT =
> 0.2340
> EAMBER (non-restraint) = -5733.2865
> Ewald error estimate: 0.4602E-02
> ------------------------------------------------------------------------------
>
> NMR restraints: Bond = 0.234 Angle = 0.000 Torsion = 0.000
> *******************
>
> 3. Now I tried with ifvari=1 and input for 10ps run is
>
> &rst
> ixpk =0, nxpk =0 iat = 3, 14, nstep1=1, nstep2=10000,
> iresid=0,irstyp=0,ifvari=1,ninc=0,imult=1,ir6=0,ifntyp=0,
> r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
> rk2=1.0000, rk3=1.0000,
> r1a=0.00000, r2a=18.0000, r3a=18.0000, r4a=99.0000,
> rk2a=1.0000, rk3a=1.0000,
> /
> ### output read correctly the input and restraint and the DUMPAVE value
> is ranging from 20-18.0 gradually through NSTEPS, and the RESTRAINT
> though decreasing has a value throughout the run of 10ps.
>
> 4. By this i understood that simple distance restraint is working but when
> tried for COM restraint with the below input
>
> &rst
> iat= -1,-1,
> iresid=1,irstyp=1,ifvari=0,ninc=0,imult=1,ir6=0,ifntyp=0,
> ^^^^^^
don't set imult=1 unless you really are sure you know what you are doing.
> r1=0.00000, r2=20.0000, r3=20.0000, r4=99.0000,
> rk2=1.0000, rk3=1.0000,
> igr1 = 1,0,
> grnam1 (1) ='CA',
^^^^
I don't think you can have a space here.
> I tried all key words
Don't just randomly try changing key words. Spend enough time with simple
things until you are confident you understand what is going on, then add
complexity one step at a time.
...dac
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Received on Sun Jun 03 2007 - 06:07:52 PDT
