AMBER Archive (2008)

Subject: AMBER: Problem running implicit minimization

From: Lili Peng (lpeng_at_ucsd.edu)
Date: Mon Mar 03 2008 - 23:10:52 CST

Dear all,

I'm having trouble running an implicit simulation. I've already minimized
my system, but sander doesn't like it when I try to run the MD. My command
line is:

/sander -O -i md.in -o nexil8_md_ini.out -c nexil8_even_min.rst -p
nexil8_even.top -r nexil8_even_md_ini.rst -x nexil8_even_md_ini.mdcrd

The error I receive is:
forrtl: severe (64): input conversion error, unit 9, file
/nas/lpeng/nexil/nexil8/nexil8_even_min.rst
Image PC Routine Line
Source
sander 0880BB22 Unknown Unknown Unknown
sander 0880A1F5 Unknown Unknown Unknown
sander 087D96E5 Unknown Unknown Unknown
sander 0879E2E2 Unknown Unknown Unknown
sander 0879E012 Unknown Unknown Unknown
sander 087B6D16 Unknown Unknown Unknown
sander 0815960A Unknown Unknown Unknown
sander 08112ED8 Unknown Unknown Unknown
sander 08111BE5 Unknown Unknown Unknown
sander 080481D5 Unknown Unknown Unknown
sander 08812AD0 Unknown Unknown Unknown
sander 08048111 Unknown Unknown Unknown

My input file is shown below. I've also attached my input .rst and
(incomplete) .out file. My .top file is ~2mb and was too big to send to the
mailing list the first time I tried to send this out.

&cntrl
  timlim = 999999., nmropt = 0, imin=0,
  ntx = 1, irest = 0, ntrx = 1, ntxo = 1,
  ntpr = 100, ntwx = 100, ntwv = 0, ntwe = 0,
  ioutfm = 0, ntwr = 50000,
  ntwprt = 0,
  ntf = 2, ntb = 0,
  igb = 2, gbsa =1, surften=0.005, dielc = 1.0,
  cut = 16.0, nsnb = 10,
  scnb = 2.0, scee = 1.2,
  nstlim = 100000, nscm = 2500, iwrap = 0,
  t = 0.0, dt = 0.002,
  temp0 = 300.0, tempi = 200.0, tautp=0.5, ig = 71227,
  heat = 0.0, ntt = 3, gamma_ln=2.0,
  ntc = 1, tol = 0.00001, jfastw = 0,
  ibelly=0, ntr=0,
&end

Any help on this problem would be appreciated.

Thanks,
Lili



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