> On Apr 19, 2015, at 9:29 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
>
> HI, all:
> I met a problem in running steered MD , I couldn't figure it out. Can
> anyone tells me what is the problem?
>
> Thank you very much
> Li
>
> *Below are the fies:*
> SMD2.in:
> #steer MD2
> &cntrl
> imin=0, irest=1, ntx=5,
> nstlim=5000, dt=0.002,
> ntt=1, ntc=2, ntf=2, ntb=1, ntp=0,
> tempi=50.0, temp0=50.0,dielc=80.0,
> ntpr=500, ntwx=500, ntwr=5000,
> ntr=1, restraint_wt=50, restraintmask=':1-469,509&!.H=', ntrx=1,
> jar=1,
> /
> &wt
> type='DUMPFREQ', istep1=1,
> /
> &wt
> type='END',
> /
> DISANG=SMD2.rst
> DUMPAVE=dist_vs_t_threepull2
> LISTIN=POUT
> LISTOUT=POUT
>
> SMD2.rst:
> #
> # 470 U O2 39 ASP O 46.3504
> &rst
> ixpk= 0, nxpk= 0, iat=7755, 661, r1= 1.30, r2= 1.80, r3=46.35, r4=46.85,
> rk2=20.0, rk3=20.0, ir6=1, ialtd=0,
> &end
This input file is wrong.
Look at chapter 21, section 7.2 (page 392 of the Amber 14 manual) for details about running steered MD. In particular, it says “Note that only r2, r2a, and rk2 are required”. From there, it builds harmonic potentials that interpolate from r2 to r2a linearly during the course of the simulation. As the default value of all variables are zero, what your input file above is doing is defining an umbrella potential around 1.8 angstroms separation between atoms 7755 and 661 with a force constant of 20 kcal/mol/A^2 and over the course of 5000 steps, reducing that distance to 0.
Look carefully at all of the input options in chapter 21.7.2, as well as the NMR options in chapter 23, so that you understand what the input file you use is actually requesting. The flat-well potential you are defining (i.e., quadratic restraint between 1.3 and 1.8 A, no restraint between 1.8 and 46.35 A, and quadratic restraint between 46.35 and 46.85 A) is unlikely to have any effect whatsoever (unless those atoms are routinely more than 46 A apart).
When you do these kinds of simulations, you should also always check the initial configuration to make sure that the starting distance is close to the center of your biasing potential. If it is not, large forces will be introduced that can destroy a simulation (in the way that you’ve seen here).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Apr 20 2015 - 06:00:06 PDT
