it will helpo us to check the files if you can explain exactly what you're
trying to do here. what is the initial structure, what is the reference
structure, what do you intend? My guess is that your initial structure and
reference structure have rmsd values that don't match your input, but
that's just a guess. maybe try running this with force constant of 0 and
ntpr=1 and see what your output tells you.
On Fri, Apr 17, 2015 at 2:45 AM, 肖立 <xiaoli19871216.gmail.com> wrote:
> Hi, all:
>
> I run targeted MD with the .in file shown as below,
>
> "
>
> #regular vacuum md, backbone restrained
>
> &cntrl
>
> imin = 0, ntx = 1, nstlim = 50000, irest=0,
>
> dt = 0.002, ntc = 2, ntf = 2,
>
> temp0 = 50.0,
>
> ntpr = 500, ntwx = 500, ntwr = 50000,
>
> ntb = 2, ntt = 3, ntp=1,
>
> nscm = 0, nmropt = 1,
>
> ntr = 1, restraint_wt=50,
>
> restraintmask=":1-94,163-469&!.H=",
>
> itgtmd = 1, tgtrmsd = 6.1919, tgtmdfrc = 5,
>
> tgtrmsmask="(:470,471,487&!.H=)|:498-499.P
> ,OP1,OP2,O5',C5',O4',C4',O3',C3',C2',C1'",
>
> /
>
> &wt
>
> TYPE='TGTRMSD', istep1=1, istep2=25000,
>
> value1 = 6.1919, value2 = 0.0,
>
> /
>
> &wt
>
> TYPE='TGTRMSD', istep1=25000, istep2=50000,
>
> value1 = 0.0, value2 = 0.0,
>
> /
>
> &wt
>
> type="END",
>
> /
>
> "
>
>
> However, it gives me the error as :
>
> "
>
> vlimit exceeded for step 48; vmax = 235.5863
>
>
> Coordinate resetting (SHAKE) cannot be accomplished,
>
> deviation is too large
>
> NITER, NIT, LL, I and J are : 0 0 3905 7743 7744
>
>
> Note: This is usually a symptom of some deeper
>
> problem with the energetics of the system."
>
>
> Could anyone tell me what's wrong with it and how to run it correctly?
>
>
> Thank you very much!
>
> --
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
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Received on Fri Apr 17 2015 - 05:30:04 PDT
