AMBER Archive (2008)

Subject: AMBER: vlimit exceeded

From: Wang,Ying (wangying_at_ufl.edu)
Date: Sat Aug 30 2008 - 10:49:03 CDT

Hi, Dear all,
I'm running a 30,000 atoms system in vacuo and get the error
messages as below:

vlimit exceeded for step 21771; vmax = 20.9636

my .in file is as below:

cell_NPT: 100ps MD
 &cntrl
  imin = 0, irest = 1, ntx = 7,
  ntb = 0,
  cut = 12, ntr=1,
  ntc = 2, ntf = 2,
  tempi = 300.0, temp0 = 300.0,
  ntt = 3, gamma_ln = 2.0,
  nstlim = 50000, dt = 0.001,
  ntpr = 1000, ntwx = 1000, ntwr = 1000
 /
keep restraints
100.0
RES 217 954
END
keep out
10.0
RES 955 1692
END
END

could you tell me how to fix it? It will be appreciated greatly!

And my second question is:
If I get the message as below
| RE_POSITION Moving by 0.063118 -3.392424 -0.241462

how can I align the .rst and .mdcrd files to let the center come
back to the oringinal position? Thanks a lot!!

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