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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Received on Wed Sep 20 2006 - 06:07:11 PDT
