oh I see - you didn't define tgtfitmask. for most cases you probbly DO want
best fit, so using nofit wouldn't make sense. I suggest removing the nofit,
and then define the tgtfitmask in sander mdin. I could help more if I knew
better what you want to do.
carlos
On Fri, Apr 17, 2015 at 1:10 PM, 肖立 <xiaoli19871216.gmail.com> wrote:
> 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
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>
>
>
> --
> Li Xiao
> University of California, Irvine
> Email: xiaoli19871216.gmail.com
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Received on Fri Apr 17 2015 - 10:30:05 PDT
