AMBER Archive (2002)

Subject: mpi version of sander in Amber 6.0 with constraints

From: Stefan Andreev Andreev (sandreev_at_fas.harvard.edu)
Date: Wed Aug 14 2002 - 17:13:26 CDT

Hello,

I tried to run the mpi version of sander on a linux machine compiled with
the portland group compilers, and it runs fine unless I impose distance
restraints throught the nmropt=1 option. If I do that, I get a
segmentation fault before any steps are evaluated. As soon as I set
nmropt=0 in the input file, the program works fine.

Using the same version of sander compiled on an SGI or on linux using g77,
it works fine, so it seems that the configuration files are fine. Has
anybody had such problems?

Thanks,

Stefan

PS: Here's the input file md.in

# # input file for SANDER
 &cntrl
      timlim = 999999.,
      imin = 0,
      nmropt = 1,
      ntx = 7,
      irest = 1,
      ntrx = 1,
      ntxo = 1,
      ntpr = 100,
      ntwr = 100,
      iwrap = 0,
      ntwx = 200,
      ntwv = 2000,
      ntwe = 1000,
      ioutfm = 0,
      ntwprt = 0,
      ntf = 1,
      ntb = 1,
      dielc = 1.0,
      igb = 0,
      cut = 10.0,
      nsnb = 10,
      scnb = 2.0,
      scee = 1.2,
      ipol = 0,
      n3b = 0,
      nion = 0,
      ibelly = 0,
      ntr = 0,
      maxcyc = 2000,
      ncyc = 10,
      ntmin = 1,
      dx0 = 0.01,
      dxm = 0.5,
      drms = 0.0001,
      nstlim = 1000,
      ndfmin = 6,
      ntcm = 1,
      nscm = 0,
      t = 0.0,
      dt = 0.002,
      temp0 = 300.0,
      tempi = 300.0,
      ig = 71277,
      heat = 0.0,
      ntt = 1,
      dtemp = 0.0,
      tautp = 0.5,
      vlimit = 0.0,
      ntp = 0,
      pres0 = 1.0,
      comp = 44.6,
      taup = 1.0,
      npscal = 1,
      ntc = 2,
      tol = 0.0005,
      jfastw = 0,
      ivcap = 0,
      matcap = 0,
      fcap = 0.0,
 &end
 &ewald
      nfft1 = 8,
      nfft2 = 8,
      nfft3 = 8,
      order = 4,
      ischrgd = 0,
      verbose = 0,
      ew_type = 0,
      dsum_tol = 0.000001,
      netfrc = 1,
 &end
 &wt
TYPE='END'
 &end
 &rst
IAT(1) = 362,
IAT(2) = 423,
IAT(3) = 0,
IAT(4) = 0,
IRESID = 0,
NSTEP1 = 0,
NSTEP2 = 0,
IRSTYP = 0,
IALTD = 0,
IFVARI = 0,
R1 = 0.,
R2 = 43,
R3 = 43,
R4 = 1.e30,
RK2 = 20.,
RK3 = 20.,
 &end

------------------------------------
Stefan Andreev
12 Oxford Street
Department of Chemistry, Box 102
Harvard University
Cambridge, MA 02138
USA

Office Tel: (617) 495-8859
Office Fax: (617) 384-7920
e-mail: sandreev_at_fas.harvard.edu