I ran MD for relaxation without TI and QMMM.
After that, I did the same simulation. But, I had exactly the same issue.
=================
Output1 from MM-side
=================
vlimit exceeded for step 101; vmax = 22.1543
vlimit exceeded for step 103; vmax = 21.3824
vlimit exceeded for step 104; vmax = 20.2245
vlimit exceeded for step 107; vmax = 21.9216
vlimit exceeded for step 108; vmax = 23.3998
vlimit exceeded for step 109; vmax = 26.7773
NSTEP = 110 TIME(PS) = 56.220 TEMP(K) = 589.52 PRESS =
1326.6
Etot = -6902.6424 EKtot = 3126.1095 EPtot =
-10028.7519
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
2003.2312
EELEC = -11914.6808 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 45.1760
EKCMT = 754.9877 VIRIAL = -1.6260 VOLUME =
26414.8298
Density =
1.0084
Ewald error estimate: 0.7794E-02
------------------------------------------------------------------------------
vlimit exceeded for step 110; vmax = 23.8606
vlimit exceeded for step 111; vmax = 21.1437
vlimit exceeded for step 112; vmax = 20.1594
NSTEP = 120 TIME(PS) = 56.240 TEMP(K) = 393.02 PRESS =
1353.6
Etot = -7966.9459 EKtot = 2084.0895 EPtot =
-10051.0354
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1998.2444
EELEC = -11876.4928 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = -21.5815
EKCMT = 731.5944 VIRIAL = -41.4536 VOLUME =
26450.7682
Density =
1.0070
Ewald error estimate: 0.8075E-02
------------------------------------------------------------------------------
vlimit exceeded for step 123; vmax = 22.7526
vlimit exceeded for step 124; vmax = 20.3639
vlimit exceeded for step 125; vmax = 22.9448
NSTEP = 130 TIME(PS) = 56.260 TEMP(K) = 493.77 PRESS =
994.1
Etot = -7417.3292 EKtot = 2618.3934 EPtot =
-10035.7225
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1947.4979
EELEC = -11810.1983 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = 13.2787
EKCMT = 781.3425 VIRIAL = 213.0164 VOLUME =
26478.4630
Density =
1.0060
Ewald error estimate: 0.7859E-02
------------------------------------------------------------------------------
NSTEP = 140 TIME(PS) = 56.280 TEMP(K) = 402.43 PRESS =
475.2
Etot = -7994.3020 EKtot = 2134.0392 EPtot =
-10128.3411
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1902.1486
EELEC = -11811.8414 EHBOND = 0.0000 RESTRAINT =
0.0000
DV/DL = -46.7121
EKCMT = 826.2157 VIRIAL = 554.3814 VOLUME =
26495.4568
Density =
1.0053
Ewald error estimate: 0.7845E-02
------------------------------------------------------------------------------
=================
Output2 form QM-side
=================
NSTEP = 110 TIME(PS) = 56.220 TEMP(K) = 314.79 PRESS =
1326.6
Etot = -8359.4551 EKtot = 1669.2968 EPtot =
-10028.7519
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
2003.2312
EELEC = -11914.6808 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -117.3023
DV/DL = 45.1760
EKCMT = 754.9877 VIRIAL = -1.6260 VOLUME =
26414.8298
Density =
1.0084
Ewald error estimate: 0.7794E-02
------------------------------------------------------------------------------
NSTEP = 120 TIME(PS) = 56.240 TEMP(K) = 307.52 PRESS =
1353.6
Etot = -8420.3371 EKtot = 1630.6983 EPtot =
-10051.0354
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1998.2444
EELEC = -11876.4928 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -172.7870
DV/DL = -21.5815
EKCMT = 731.5944 VIRIAL = -41.4536 VOLUME =
26450.7682
Density =
1.0070
Ewald error estimate: 0.8075E-02
------------------------------------------------------------------------------
NSTEP = 130 TIME(PS) = 56.260 TEMP(K) = 311.32 PRESS =
994.1
Etot = -8384.8390 EKtot = 1650.8836 EPtot =
-10035.7225
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1947.4979
EELEC = -11810.1983 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -173.0222
DV/DL = 13.2787
EKCMT = 781.3425 VIRIAL = 213.0164 VOLUME =
26478.4630
Density =
1.0060
Ewald error estimate: 0.7859E-02
------------------------------------------------------------------------------
NSTEP = 140 TIME(PS) = 56.280 TEMP(K) = 316.07 PRESS =
475.2
Etot = -8452.2589 EKtot = 1676.0823 EPtot =
-10128.3411
BOND = 0.0000 ANGLE = 0.0000 DIHED =
0.0000
1-4 NB = 0.0000 1-4 EEL = 0.0000 VDWAALS =
1902.1486
EELEC = -11811.8414 EHBOND = 0.0000 RESTRAINT =
0.0000
PM3ESCF= -218.6483
DV/DL = -46.7121
EKCMT = 826.2157 VIRIAL = 554.3814 VOLUME =
26495.4568
Density =
1.0053
Ewald error estimate: 0.7845E-02
------------------------------------------------------------------------------
On Mon, May 17, 2010 at 2:01 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
> > > Density = 0.6778
> > The system has 2668 atoms. The first atom is Mg2+ and the following 18
> > atoms belong to the water molecules of the complex. The rest of them are
> > all solvent water molecules.
>
> I wonder what would happen if you equilibrated density first.
> I.e. constant pressure until density ~= 1.
>
> Bill
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Best,
InSuk Joung
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Received on Mon May 17 2010 - 11:30:06 PDT
