Hi,all:
Recently, I was running the POL3 bulk water using amber11, though i can pass the minimization, when i run the NVT simulation, something strange happened.... NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 0.00 PRESS = 0.0 Etot = -19178.2762 EKtot = 0.0000 EPtot = -19178.2762 BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = 5804.4498 EELEC = -18269.6643 EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = -6713.0617 Dipole convergence: rms = 0.416E-04 iters = 8.00 ------------------------------------------------------------------------------
vlimit exceeded for step 1; vmax = 37.6326vlimit exceeded for step 2; vmax = **********vlimit exceeded for step 3; vmax = **********vlimit exceeded for step 4; vmax = **********vlimit exceeded for step 5; vmax = **********vlimit exceeded for step 6; vmax = **********vlimit exceeded for step 7; vmax = **********
NSTEP = 100 TIME(PS) = 0.100 TEMP(K) =453529.68 PRESS = 0.0 Etot = NaN EKtot = 3209352.6744 EPtot = NaN BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = ************** EELEC = NaN EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = NaN Dipole convergence: rms = NaN iters = 21.00 ------------------------------------------------------------------------------
NSTEP = 200 TIME(PS) = 0.200 TEMP(K) =453529.68 PRESS = 0.0 Etot = NaN EKtot = 3209352.6744 EPtot = NaN BOND = 0.0000 ANGLE = 0.0000 DIHED = 0.0000 1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS = ************** EELEC = NaN EHBOND = 0.0000 RESTRAINT = 0.0000 EPOLZ = NaN Dipole convergence: rms = NaN iters = 21.00
the energy and temperature are unnormal for all steps except for the first snapshot, my in file(md0.in) is....
polyA-polyT 10-mer: &cntrl imin = 0, irest = 0, ntx = 1, ntb = 1, cut = 10, ntr = 0, ntc = 2, ntf = 2, tempi = 0.0, temp0 = 300.0, tautp =0.5, ntt = 3, gamma_ln = 1.0, nstlim = 150000, dt = 0.001, ig = -1, ntpr = 100, ntwx = 10000, ntwr = 1000 ipol=1, / &ewald indmeth=1, skinnb = 1.0, diptau = 9.9, irstdip = 0, /
MY command is : sander.MPI -O -i md0.in -p pep.parm7 -c min1.rst -ref min1.rst -rdip 1ubq.rstdip0 -o md0.out -x md0.crd -r md0.rst can anybody tell me the reason? WHAT SHOULD I DO? thx in advance.PS: the restart file of minimization(min1.rst), the result file of NVT (md0.out)and the parm file(pep.parm7) are in the attachment!
Xiaoxudong.ECNU.
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Received on Tue Sep 11 2012 - 04:00:03 PDT
