AMBER Archive (2006)

Subject: AMBER: Restart problem on PMEMD with position restraint.

From: Chunhu Tan (tanc_at_uci.edu)
Date: Mon Sep 18 2006 - 12:46:35 CDT

Hi, All,

   I got a Vlimit error when I wanted to restart a PMEMD simulation with
position restraint. My system is protein G solvated in a TIP3P water box
with 11 angstroms buffer. After the minimization, I first run 20ps NVT
simulation, then 20ps NPT simulation. All these were OK, but when I
wanted to restart the NPT simulation, I got the Vlimit error, even I
used exact the same input file as the first NPT run.
   I am using AMBER9, and here are the inputs:
 
1) MD_NVT.IN
  &cntrl
   imin = 0,
   irest = 0, ntx = 1,
   ntb = 1,
   ntt = 3, gamma_ln =1.0,
   iwrap = 1,
   ntf = 2, ntc = 2, tol = 0.000001,
   temp0 = 300, tempi = 300,
   nstlim= 10000,
   ntpr = 1000, ntwr = 1000, ntwx = 10000,
   dt = 0.002,
   cut = 9,
   ntr = 1
 /
 &ewald
  skinnb = 1.
 /
Hold the protein fixed
50.0
RES 1 56
END

_______________________________________
2) MD_NPT.IN
&cntrl
   imin = 0,
   irest = 1, ntx = 5,
   ntb = 2, ntp = 1,
   ntt = 1, iwrap = 1,
   ntf = 2, ntc = 2, tol = 0.000001,
   temp0 = 300,
   nstlim= 10000,
   ntpr = 5000, ntwr = 5000, ntwx = 200000,
   dt = 0.002,
   cut = 9,
   ntr = 1
 /
 &ewald
  skinnb = 1.
 /
Hold the nucleic acid fixed
50
RES 1 56
END
END

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