[AMBER] [ MD Failure ]

From: 조준범 <j1300704.gmail.com>
Date: Mon, 13 Jan 2020 01:19:33 +0900

Hi all,

I made polymer through tleap and combined polymers and ionic liquids. EM
was operated but LINMIN FAILURE occurs sometimes. However, energy profile
seems reasonable.

It is problem that once I operate NPT simulation, it crushes immediately.

What can be the solution?

The logs of EM and NPT are shown below.

< 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

     ... RESTARTED DUE TO LINMIN FAILURE ...

     ... RESTARTED DUE TO LINMIN FAILURE ...

     ***** REPEATED LINMIN FAILURE *****

     ***** SEE http://ambermd.org/Questions/linmin.html FOR MORE INFO *****


                    FINAL RESULTS



   NSTEP ENERGY RMS GMAX NAME NUMBER
  90347 -4.4726E+03 2.2279E-03 3.3067E-02 S1 4978

 BOND = 27.8763 ANGLE = 400.3410 DIHED =
 700.4777
 VDWAALS = -563.3840 EEL = -2895.5813 HBOND =
 0.0000
 1-4 VDW = 610.9668 1-4 EEL = -2561.4514 RESTRAINT =
 0.0000
 EPOLAR = -191.8183
 Dipole convergence: rms = 0.169E+00 temperature = 0.00

< NPT >
--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

| # of SOLUTE degrees of freedom (RNDFP): 16017.
| # of SOLVENT degrees of freedom (RNDFS): 0.
| NDFMIN = 16014. NUM_NOSHAKE = 0 CORRECTED RNDFP = 16014.
| TOTAL # of degrees of freedom (RNDF) = 16014.
 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
| CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 688445
| TOTAL SIZE OF NONBOND LIST = 688445

 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
 ------------------------------------------------------------------------------
-- 
*Junbeom Cho*
Integrated Ph. D. Student
Theoretical and Computational Soft Matters Laboratory
School of Chemical and Biological Engineering
Seoul National University
1, Gwanak-ro, Gwanak-gu, Seoul, 08826, Korea
Tel: +82-2-880-1529
E-mail: cjb0704.snu.ac.kr
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Received on Sun Jan 12 2020 - 08:30:01 PST
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