check the archives- there are limits on line length. if you want to
pick all atoms, why not just specify residues and skip the atom name
list?
regarding the vlimit error, look at the initial energies. perhaps your
initial restraint forces are too high. you might want to vary the
target rmsd value with time if the structures are far apart.
On Wed, Feb 25, 2009 at 4:34 AM, balaji nagarajan
<balaji_sethu.hotmail.com> wrote:
>
> Dear Amber ,
>
> I tried Targeted Molecular Dynamics
> by giving the mask to all the atoms
> and i gave all the atom flags in the input
> the total number of atoms are 1296
> but when i run the script it shows
> only 1062 atoms matches
>
>
> my input file is as follows
>
> &cntrl
> imin = 0,
> irest = 0 ,
> ntb = 0,
> ntxo = 1,
> ntx =1,
> tempi =300.0
> ntb = 0,
> ntc=2,
> ntr =0,
> ntf = 2,
> igb = 1,
> nscm = 100,
> ntwr = 1000
> ntpr = 100,
> ntwx = 100,
> ntwv =100,
> ntwe = 100,
> ntt = 3,
> gamma_ln = 1.0,
> temp0 = 300.0
> nstlim = 10000,
> dt = 0.001,
> cut = 999,
> itgtmd=1,
> tgtrmsd =0.5 ,
> tgtmdfrc = 10.0,
> tgtfitmask= ":1-40 . P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4',H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7,O6,H1,N2,1H2,2H2,C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
> tgtrmsmask= ":1-40 . P,O1P,O2P,O5',C5',C4',O4',C1',C6,C5,C2,O2,C4,C3',C2',O3',H5T,1H5',2H5',H4',H1',N1,C6,H6,H5,N4,1H4,2H4,N3,H3',1H2',2H2',N9,C8,H8,N7, O6,H1,N2,1H2,2H2,C7,1H7,2H7,3H7,O4,H3,N6,1H6,2H6,H2,H3T,Na+",
> /
>
>
>
>
> and the run got stopped with the error
> --------------------------------------------
> vlimit exceeded for step 34; vmax = 20.9476
>
> Coordinate resetting (SHAKE) was not accomplished
> within 3000 iterations
>
> Note: This is usually a symptom of some deeper
> problem with the energetics of the system.
> ----------------------------------------------------------------------
> Is there any problem in the mask atom flags !
>
> what does this error mean !
>
> thanks in advance
> balaji
> UOM
>
>
>
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Received on Wed Feb 25 2009 - 08:25:19 PST
