Dear all,
I want to preform a MD calculation of my protein, but there are problems that have bothered me for a long time. After I minimized, heated and equilibrated the system before the MD, there is no problem. Then the MD calculation always stopped with a SHAKE error and many vlimit reminds. I have searched on the Internet and mailing list, and tried heating slowly and did the MD with a smaller timestep(0.5 fs), the problem still exist with many vlimit reminders. What can I do now? Look forward to your reply. The input and output files are shown here:
min1:
minimization solvent + ions
&cntrl
IMIN = 1,
MAXCYC = 1000,
NCYC = 500,
NTB = 1,
NTR = 1,
CUT = 10.0
/
Hold the protein fixed
500.0
RES 1 350
END
END
min2:
minimization whole system
&cntrl
IMIN = 1,
MAXCYC = 10000,
NCYC = 5000,
NTB = 1,
NTR = 0,
CUT = 10.0
/
Heat:
Heat 20ps from 0 to 100K
&cntrl
IMIN = 0,NTX = 1,IREST = 0,
NTPR = 500,
NTR = 1,
RESTRAINT_WT = 10.0,
RESTRAINTMASK = ':1-350',
NSTLIM = 40000,DT = 0.0005,NTWR = 500,NTWX =500,
tempi = 0.0,temp0 = 100,ntt = 3,gamma_ln = 2.0,nmropt=1,ntp = 0,
nrespa=1,ntc=2,ntf=2,
NTB = 1,
CUT = 10.0,
ig = -1,
/
&wt type='TEMP0',istep1=0,istep2=40000,value1=0.0,value2=100 /
&wt type='END' /
Heat 80ps from 100 to 300K
&cntrl
IMIN = 0,NTX = 5,IREST = 1,
NTPR = 500,
NTR = 1,
RESTRAINT_WT = 10.0,
RESTRAINTMASK = ':1-350',
NSTLIM = 160000,DT = 0.0005,NTWR = 500,NTWX =500,
tempi = 100.0,temp0 = 300.0,ntt = 3,gamma_ln = 2.0,nmropt=1,
nrespa=1,ntc=2,ntf=2,
NTP = 0,NTB = 1,
CUT = 10.0,
ig = -1,
/
&wt type='TEMP0',istep1=0,istep2=160000,value1=100.0,value2=300.0 /
&wt type='END' /
with a weaker res:
100ps at 300K
&cntrl
IMIN = 0,NTX = 5,IREST = 1,
NTPR = 500,NTWR = 500,NTWX =500,
NTR = 1,
NSTLIM = 100000,DT = 0.001,
temp0 = 300.0,ntt = 3,gamma_ln = 2.0,
ntc=2,ntf=2,
NTB = 1,ntp = 0,
CUT = 10.0,
ig = -1,
/
fix protein
5.0
RES 1 350
END
END
100ps at 300K
&cntrl
IMIN = 0,NTX = 5,IREST = 1,
NTPR = 500,NTWR = 500,NTWX =500,
NTR = 1,
NSTLIM = 100000,DT = 0.001,
temp0 = 300.0,ntt = 3,gamma_ln = 2.0,
ntc=2,ntf=2,
NTB = 1,ntp = 0,
CUT = 10.0,
ig = -1,
/
fix protein
1.0
RES 1 350
END
END
Equilibration:NVT+NPT
100ps at 300K
&cntrl
IMIN = 0,NTX = 5,IREST = 1,
NTPR = 500,NTWR = 500,NTWX =500,
NTR = 0,
NSTLIM = 200000,DT = 0.0005,
temp0 = 300.0,ntt = 3,gamma_ln = 2.0,
ntc=2,ntf=2,
NTB = 1,ntp = 0,
CUT = 10.0,
ig = -1,
/
100ps at 300K
&cntrl
IMIN = 0,NTX = 5,IREST = 1,
NTPR = 500,NTWR = 500,NTWX =500,
NTR = 0,
NSTLIM = 200000,DT = 0.0005,
temp0 = 300.0,ntt = 3,gamma_ln = 2.0,
ntc=2,ntf=2,
ntp = 1,NTB = 2,pres0 = 1.0,taup = 2.0,
CUT = 10.0,
ig = -1,
/
Production:
1ns at 300K
&cntrl
IMIN = 0,NTX = 5,IREST = 1,
NTPR = 500,NTWR = 500,NTWX =500,
NTR = 0,
NSTLIM = 1000000,DT = 0.001,
temp0 = 300.0,ntt = 3,gamma_ln = 2.0,
ntc=2,ntf=2,
ntp = 1,NTB = 2,pres0 = 1.0,taup = 2.0,
CUT = 10.0,
ig = -1,
/
output:
vlimit exceeded for step 4009; vmax = 22.2879
vlimit exceeded for step 4010; vmax = 23.3784
vlimit exceeded for step 4012; vmax = 24.6563
vlimit exceeded for step 4013; vmax = 20.5937
vlimit exceeded for step 4016; vmax = 20.4398
vlimit exceeded for step 4017; vmax = 20.0801
vlimit exceeded for step 4018; vmax = 20.5544
vlimit exceeded for step 4023; vmax = 20.7146
vlimit exceeded for step 4024; vmax = 21.0257
vlimit exceeded for step 4026; vmax = 28.1213
vlimit exceeded for step 4027; vmax = 23.1559
vlimit exceeded for step 4029; vmax = 29.6555
vlimit exceeded for step 4037; vmax = 39.9303
vlimit exceeded for step 4038; vmax = 23.4022
vlimit exceeded for step 4039; vmax = 1314.8956
vlimit exceeded for step 4040; vmax = 43.5985
Coordinate resetting (SHAKE) cannot be accomplished,
deviation is too large
NITER, NIT, LL, I and J are : 0 2 2672 5501 5502
Note: This is usually a symptom of some deeper
problem with the energetics of the system.
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Received on Sun Sep 20 2015 - 19:00:04 PDT
