AMBER Archive (2003)

Subject: MD went crazy

From: Youyi Peng (pengyo_at_UMDNJ.EDU)
Date: Fri Apr 18 2003 - 10:20:25 CDT

Hi,
  I initiated MD by heating the ligand-protein complex with no
constraints on the atoms from 0 to 300K in 10 ps.Then 100ps eqilibration
at the constant temp. 300K was performed on restrained backbone and
distance. I got crazy MD output. THe energy and temp. went to very high
and a lot of vlimit warnings. Below is the input file and part of the
output file. Please take a look for me.
 Thank you very much and happy good Friday!

MDIN:
dynamics w/o belly on protein, 9.0 cut, with constraints of backbone and
distance
 &cntrl
  nmropt = 1,
  ntx = 5, irest = 1, ntrx = 1, ntxo = 1,
  ntpr = 1000, ntwx = 1000, ntwv = 0, ntwe = 0,

  ntf = 1, ntb = 0,
  cut = 9.0, nsnb = 10, dielc=4.0

  ibelly = 0, ntr = 1,

  imin = 0,
  nstlim = 100000,
  nscm = 0, dt = 0.001,

  temp0 = 300.0, tempi = 300.0,
   heat = 0.0,
  ntt = 1,
  tautp = 2.0,
  vlimit = 20.0,

  ntc = 1, tol = 0.00001,
 &end

 &ewald
   eedmeth=5,
 &end

 &wt
   type='END' ,
 &end

LISTOUT=POUT
DISANG=RST.dist

Hold the backbone restrainted
500.0
FIND
 * CT * *
 * N * *
 * C * *
 * O * *
SEARCH
RES 1 293
END
END

OUTPUT
vlimit exceeded for step 992; vmax = 1297679.08
 vlimit exceeded for step 993; vmax = 200557512.
 vlimit exceeded for step 994; vmax = 86296.6221
 vlimit exceeded for step 995; vmax = 530655.444
 vlimit exceeded for step 996; vmax = 719129.926
 vlimit exceeded for step 997; vmax = 2.54845046E+09
 vlimit exceeded for step 998; vmax = 97404.1622
 vlimit exceeded for step 999; vmax = 330667.274

NSTEP = 1000 TIME(PS) = 11.000 TEMP(K) =********* PRESS = 0.0

 Etot = ************ EKtot = ************ EPtot =
3906732.9101
 BOND = 865895.1848 ANGLE = 223527.1116 DIHED =
15612.3010
 1-4 NB = 1509819.0853 1-4 EEL = 546.5250 VDWAALS =
163607.4823
 EELEC = -1106.9859 EHBOND = 0.0000 RESTRAINT =
1128832.2060
 EAMBER (non-restraint) = 2777900.7040