HI. Calos:
Thank you for the reply. You are right, my initial rmsd is wrong since I
didn't turn nofit on when using cpptraj to measure it. It works normal now.
Thank you very much!
Li
On Fri, Apr 17, 2015 at 5:24 AM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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--
Li Xiao
University of California, Irvine
Email: xiaoli19871216.gmail.com
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Received on Fri Apr 17 2015 - 10:30:04 PDT
