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Minimize with Movable Boundary Conditions?
#1391 05/08/04 05:51 PM
Joined: Feb 2004
Posts: 13
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I have been having a lot of problems with pressure (huge negative pressures, huge positive pressures, huge swings). In the "large negative pressures" thread under MD, it was suggested that my problems may be due to inadequate minimization. I have used cascaded minimizations (sd, conj, abnr) to a tolgrd of 0.05. I think that the problem is that if the volume is wrong when I define my crystal, minimization won't help (unless there is a way to due cpt minimization, which is my question).

ABNER> Minimization exiting with gradient tolerance ( 0.0500000) satisfied.

ABNR MIN: Cycle ENERgy Delta-E GRMS Step-size
ABNR INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
ABNR EXTERN: VDWaals ELEC HBONds ASP USER
ABNR IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
---------- --------- --------- --------- --------- ---------
ABNR> 32-177866.01670 14.90206 0.04467 0.01178
ABNR INTERN> 3209.47440 3031.88293 618.99653 3654.51374 12.14728
ABNR EXTERN> 15524.13893-185757.10293 0.00000 0.00000 0.00000
ABNR IMAGES> 855.25041 -19015.31800 0.00000 0.00000 0.00000
---------- --------- --------- --------- --------- ---------

CHARMM> Dynamics cpt -
CHARMM> leap STRT NSTEP 2500 TIMESTEP 0.0010 -
CHARMM> inbfrq -1 ihbfrq 0 ilbfrq 0 -
CHARMM> IUNCRD -1 IUNVEL -1 KUNIT 50 IUNWRI -1 IUNREA -1 -
CHARMM> IPRFRQ 100 NPRINT 250 NSAVC 0 NSAVV 0 -
CHARMM> IASORS 1 IASVEL 1 NTRFRQ 1500 -
CHARMM> FIRSTT 12.0 FINALT @cooltemp TEMINC 12.0 -
CHARMM> IHTFRQ 50 IEQFRQ 0 ICHECKW 0 TWINDH 10.0 TWINDL -10.0 -
CHARMM> cutim @look cutnb @look ctonnb @on ctofnb @off switch vswitch -
CHARMM> !ewald pmewald kappa @kap fftx @2 ffty @3 fftz @4 order 6 -
CHARMM> ISEED 314159 -
CHARMM> !kappa between 4/cutoff & 5/cutoff
CHARMM> pconstant pmzz 10000.0 pmyy 0.0 pmxx 0.0 pgamma 20.0 pref 1.0
Parameter: COOLTEMP -> "300"
Parameter: LOOK -> "15.5"
Parameter: LOOK -> "15.5"
Parameter: ON -> "13"
Parameter: OFF -> "14"
IUNREA = -1 IUNWRI = -1 IUNOS = -1
IUNCRD = -1 IUNVEL = -1 KUNIT = 50

SELECTED IMAGES ATOMS BEING CENTERED ABOUT 0.000000 0.000000 0.000000

NONBOND OPTION FLAGS:
ELEC VDW ATOMs CDIElec SWITch VATOm VSWItch
BYGRoup NOEXtnd NOEWald
CUTNB = 15.500 CTEXNB =999.000 CTONNB = 13.000 CTOFNB = 14.000
WMIN = 1.200 WRNMXD = 0.500 E14FAC = 1.000 EPS = 1.000
NBXMOD = 5
There are 10078884 atom pairs and 34648 atom exclusions.
There are 0 group pairs and 948 group exclusions.
DCNTRL> Constant pressure requested.
Reference pressure tensor (XX,YY,ZZ)= 1.0 1.0 1.0 atm.

Reference pressure tensor (XY,XZ,YZ)= 0.0 0.0 0.0 atm.

NSTEP = 2500 NSAVC = 0 NSAVV = 0
ISCALE = 0 ISCVEL = 0 IASORS = 1
IASVEL = 1 ICHECW = 0 NTRFRQ = 1500
IHTFRQ = 50 IEQFRQ = 0 NPRINT = 100
INBFRQ = -1 IHBFRQ = 0 IPRFRQ = 100
ILBFRQ = 0 IMGFRQ = 50 ISEED = 314159
ISVFRQ = 0 NCYCLE = 50 NSNOS = 10
FIRSTT = 12.000 TEMINC = 12.000 TSTRUC = -999.000
FINALT = 300.000 TWINDH = 10.000 TWINDL = -10.000

TIME STEP = 2.04548E-02 AKMA 1.00000E-03 PS

NUMBER OF DEGREES OF FREEDOM = 60480

SEED FOR RANDOM NUMBER GENERATOR IS 314159
GAUSSIAN OPTION IS 1
VELOCITIES ASSIGNED AT TEMPERATURE = 15.0000

DETAILS ABOUT CENTRE OF MASS
POSITION : 5.85243132E-02 -2.41075936E-02 -0.99846208
VELOCITY : -5.40108942E-04 -3.43435621E-04 3.71813709E-04
ANGULAR MOMENTUM : -2243.6249 -6326.6543 1235.3192
KINETIC ENERGY : 4.28568114E-02
DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
---------- --------- --------- --------- --------- ---------
DYNA> 0 0.00000-186579.84051 905.69811-187485.53862 15.07169
DYNA PROP> 61.06686-185405.97214 4427.30324 1173.86838-678846.63425
DYNA INTERN> 3209.47440 3031.88293 618.99653 3654.51374 12.14728
DYNA EXTERN> 15513.06575-193301.45559 0.00000 0.00000 0.00000
DYNA IMAGES> 866.32359 -21090.48725 0.00000 0.00000 0.00000
DYNA PRESS> -934715.440591387279.86343 304981.25171 453608.11836 210150.00770
---------- --------- --------- --------- --------- ---------
Crystal Parameters : Crystal Type = ORTH
DYNA A = 29.96920 B = 28.83780 C = 243.16000
DYNA Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000
DYNA PIXX = 580261.96 PIYY = 267243.12 PIZZ = 513319.28
DYNA PIXY = 6954.62 PIXZ = 9374.36 PIYZ = 13046.60
DYNA Gradient Norm = **********

UPDECI: Nonbond update at step 5
UPDECI: Nonbond update at step 9
UPDECI: Nonbond update at step 12
UPDECI: Nonbond update at step 15
UPDECI: Nonbond update at step 18
UPDECI: Nonbond update at step 21
UPDECI: Nonbond update at step 24
UPDECI: Nonbond update at step 27
UPDECI: Nonbond update at step 30
UPDECI: Nonbond update at step 33
UPDECI: Nonbond update at step 36
UPDECI: Nonbond update at step 39
UPDECI: Nonbond update at step 42
UPDECI: Nonbond update at step 45
UPDECI: Nonbond update at step 48

SEED FOR RANDOM NUMBER GENERATOR IS 1760683777
GAUSSIAN OPTION IS 1
VELOCITIES ASSIGNED AT TEMPERATURE = 24.0000

DETAILS ABOUT CENTRE OF MASS
POSITION : 5.84574895E-02 -2.31714705E-02 -0.99766952
VELOCITY : -5.34658108E-05 6.64593002E-04 -7.71902176E-07
ANGULAR MOMENTUM : 6477.6619 11706.324 1927.9392
KINETIC ENERGY : 3.47715104E-02
DYNA DYN: Step Time TOTEner TOTKe ENERgy TEMPerature
DYNA PROP: GRMS HFCTote HFCKe EHFCor VIRKe
DYNA INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
DYNA EXTERN: VDWaals ELEC HBONds ASP USER
DYNA IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
DYNA XTLE: XTLTe SURFtension XTLPe XTLtemp
---------- --------- --------- --------- --------- ---------
DYNA> 50 0.05000-518815.23776 1445.81083-520261.04860 24.05969
DYNA PROP> 88.32807-515920.26164 10130.73921 2894.97612 345482.32428
DYNA INTERN> 82990.26346 53762.53083 1507.69054 5964.49247 761.50415
DYNA EXTERN> 56301.62663-455999.24142 0.00000 0.00000 0.00000
DYNA IMAGES> 5943.44248-271493.35772 0.00000 0.00000 0.00000
DYNA PRESS> -143004.37757 -87317.17196 46633.62278 -26271.64806 210268.06230
DYNA XTLE> -187556.43491 99097.48490 3.06651 52769.43217
---------- --------- --------- --------- --------- ---------
Crystal Parameters : Crystal Type = ORTH
DYNA A = 29.96920 B = 28.83780 C = 243.29660
DYNA Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000
DYNA PIXX = 40722.39 PIYY = -144309.81 PIZZ = 24772.48
DYNA PIXY = -32624.07 PIXZ = 9584.73 PIYZ = -23712.11
DYNA Gradient Norm = 5412.05481

Thank you very much for your help,

Jim Sullivan


Molecular Engineering Laboratory University of Washington
Re: Minimize with Movable Boundary Conditions?
jimpsull #1392 05/09/04 07:20 PM
Joined: Sep 2003
Posts: 250
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Joined: Sep 2003
Posts: 250
Hi,

perhaps a way to get around your problems is the following recipe:

1. Minimize solvent - keep solute fixed.
2. Do cpt-dynamics (20-30 ps at 300 K.) while still keeping the solute frozen. In this way, the solvent can adjust to the potential felt by the protein.
3. Minimize solute and solvent - might be useful to introduce a harmonic restraint on the solute and scale down the force constant during the minimization procedure.
4. Heat up and run MD.


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