AMBER Archive (2007)

Subject: AMBER: vlimit exceeded for the step

From: Sudha Mani Karra (karra.md_at_gmail.com)
Date: Fri Aug 10 2007 - 14:31:08 CDT

Hey All,
          I am new to run MD simulations using AMBER package.
 I get the following error when I run a NPT simulation. The system that I am
using as the input is taken from a NVT run for 4ns.

INPUT file:
water MD run-Newtonian dynamics-berendsen- temp and press coupl
 &cntrl
  imin = 0,
  irest = 1,
  ntx = 7,
  ntpr = 100,
  ntwx = 100,
  ntwr = 1000,
  ntb = 2,
  ntf = 2,
  ntc = 2,
  cut = 7.0,
  igb = 0,
  nstlim = 2000000,
  dt = 0.002,
  ntt = 2,
  ig = 71277,
  tautp = 1.0,
  tempi = 300.0,
  temp0 = 300.0,
  vlimit = 20,
  pres0 = 1.0,
  ntp = 2,
  taup = 1.0
 /
mdrun.err ( error file):

Warning: No xauth data; using fake authentication data for X11 forwarding.
Warning: No xauth data; using fake authentication data for X11 forwarding.
Warning: No xauth data; using fake authentication data for X11 forwarding.
Killed by signal 2.
Killed by signal 2.
forrtl: error (69): process interrupted (SIGINT)
Killed by signal 2.

mdrun.out ( last lines of this file):

Exited with exit code 1.

Resource usage summary:

    CPU time : 209.55 sec.
    Max Memory : 20 MB
    Max Swap : 323 MB

    Max Processes : 9
    Max Threads : 9

The output (if any) follows:

p0_1089: p4_error: interrupt SIGSEGV: 11
p2_19438: p4_error: interrupt SIGSEGV: 11
p3_19460: p4_error: interrupt SIGSEGV: 11
p0_1089: (346.199219) net_send: could not write to fd=4, errno = 32

PS:

Read file <mdrun.err> for stderr output of this job.

filename.out (last lines of the filename.out file):

NSTEP = 57500 TIME(PS) = 4115.000 TEMP(K) = 346.28 PRESS =
12.6
 Etot = -1549.1138 EKtot = 444.8749 EPtot = -
1993.9887
 BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
283.9977
 EELEC = -2277.9864 EHBOND = 0.0000 RESTRAINT =
0.0000
 EKCMT = 220.9979 VIRIAL = 219.2103 VOLUME =
6561.5010
                                                    Density =
0.9848
 Ewald error estimate: 0.2671E-03

 vlimit exceeded for step 57542 ; vmax = 21.0570199902868
 vlimit exceeded for step 57543 ; vmax = 32.5515081029843

Could anyone please let me know how to solve this problem??
Thanks in advance,
Suma

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