On Mon, Jan 13, 2020, 조준범 wrote:
>
>I made polymer through tleap and combined polymers and ionic liquids. EM
>was operated but LINMIN FAILURE occurs sometimes. However, energy profile
>seems reasonable.
>
>< EM >
> NSTEP ENERGY RMS GMAX NAME NUMBER
> 90300 -4.4726E+03 3.1246E-03 1.3374E-01 S1 4978
>
> BOND = 27.8764 ANGLE = 400.3408 DIHED = 700.4772
> VDWAALS = -563.3815 EEL = -2895.5818 HBOND = 0.0000
> 1-4 VDW = 610.9665 1-4 EEL = -2561.4520 RESTRAINT = 0.0000
> EPOLAR = -191.8186
> Dipole convergence: rms = 0.169E+00 temperature = 0.00
>
> NSTEP = 0 TIME(PS) = 0.000 TEMP(K) = 424.46 PRESS = NaN
> Etot = NaN EKtot = 5353.1271 EPtot = NaN
> BOND = 27.8763 ANGLE = 400.3410 DIHED = 700.4777
> 1-4 NB = 1221.9335 1-4 EEL = -3242.7424 VDWAALS = -592.7252
> EELEC = NaN EHBOND = 0.0000 RESTRAINT = 0.0000
> EKCMT = 66.7873 VIRIAL = NaN VOLUME = 359686.6501
> EPOLZ = NaN
> Dipole convergence: rms = NaN temperature = 0.00
> Density = 0.1457
I don't think we can tell much from this information. The difference in
1-4 NB is probably from a different value of scnb in the two runs. The
vdW difference could be a difference in cutoff. But
it looks like the coordinates are slightly different.
Hard to say what is making EELEC in the MD run to be NaN. Very few
people use polarizable potentials in Amber, but they should work.
Compare your inputs to those in the test cases, esp. dna_pol, ff12pol,
and polarizable water. See if you can see differences between the test
examples and what you are doing. (And be sure to run these test cases,
if you have not already done so.)
Minor points: start with NVT, not NPT. Your density is very low: is it
about what you want it to be? It looks like you have lots of
non-standard pieces here, so you may need to learn a lot about the
internals of Amber to debug this. I suggest making sure a
non-polarizable short MD run will work, then turning on polarizability.
....dac
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Received on Mon Jan 13 2020 - 06:30:05 PST
