GCMC simulation of crystal water - 10/23/20 10:40 AM
Hello Charmm users,
I'm currently using Grand canonical monte carlo ensemble to simulate crystal water by inserting and deleting water atoms inside a crystal. The crystal.crd contains position of crystal atoms as well as H2O. crystal atoms are fixed and set inactive. I got an error of
MC E ENR: Eval# ENERgy Delta-E GRMS
MC E INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MC E EXTERN: VDWaals ELEC HBONds ASP USER
MC E IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
MC E EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
MC E PRESS: VIRE VIRI PRESSE PRESSI VOLUme
MC E LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
MC E> 0 28693807.808 0.000 39991243.434
MC E INTERN> 39.71400 71.43027 9.33503 125.67478 2.99950
MC E EXTERN> 157.74161 -227.80326 0.00000 0.00000 0.00000
MC E IMAGES> 28694837.626 -689.860 0.000 0.000 0.000
MC E EWALD> 43.99046 -3024.23481 2466.52214 0.00000 0.00000
MC E PRESS> -0.52165E+10 0.11479E+09 0.13065E+12 0.28750E+10 0.27377E+04
MC E LRCor> -5.32850 -10.65528
---------- --------- --------- --------- --------- ---------
***** LEVEL 2 WARNING FROM *****
***** REACHED GCMC LIMIT
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5
My scripts are like following:
*gcmc test simulation
*
!--- Read parameters, psf and coordinates
open read card name "top_all36_prot.rtf" unit 25
read rtf card unit 25
close unit 25
open read card name "par_all36m_prot.prm" unit 25
read parameter card unit 25 flex
close unit 25
stream toppar_water_ions.str
set cutnb 16.0 ! cutnb
set ctonnb 10.0 ! ctonnb
set ctofnb 12.0 ! ctofnb
set eatom atom
set etrun switch
set vatom vatom
set vtrun vswitch
OPEN UNIT 1 FORM READ NAME unit.psf
READ PSF CARD UNIT 1
CLOSe UNIT 1
! Read coordinates of starting structure
OPEN READ CARD UNIT 1 NAME crystal.crd
READ COOR CARD UNIT 1
CLOSE UNIT 1
!Set the active and blocking atoms
SCALar GCMC SET 0.0 SELEct IRES 1:12 END ! ires 1 to 12 is crystal
SCALar GCMC SET 1.0 SELEct IRES 13:42 END ! ires 13 to 42 is water
SCALar GCBLocker SET 1.0 SELEct all end
crystal define HEXAgonal 24.0709 24.0709 5.4560 90.00 90.00 120.00
crystal build noper 0 cutoff 30
update inbfrq -1 imgfrq -1 ihbfrq 0 imall -
ewald pmewald kappa 0.34 fftx 32 ffty 32 fftz 32 order 6 lrc -
@eatom @etrun @vatom @vtrun cutnb @cutnb ctonnb @ctonnb ctofnb @ctofnb -
cutim 999
ENERGY
! Create the MC move set
! Rigid translations
MOVE ADD MVTP RTRN BYREsidue WEIGht 1.0 DMAX 0.25 -
SELE (TYPE OH2) END LABEl DISP
! Rigid rotations
MOVE ADD MVTP RROT BYREsidue WEIGht 1.0 DMAX 30.0 -
SELE (TYPE OH2) END LABEl ROTA
! Insertion and deletion
MOVE ADD MVTP GCMC WEIGht 1.0 SELE (TYPE OH2) END LABEl GCMC
! Link the GCMC moves to the rotations and displacements to avoid moving
! inactive molecules.
MOVE LINK GCMC LAB1 GCMC LAB2 DISP
MOVE LINK GCMC LAB1 GCMC LAB2 ROTA
! Link the translations and rotations to each other for greater efficiency
MOVE LINK LAB1 DISP LAB2 ROTA
OPEN WRITE UNFOrmatted UNIT 32 NAME gcmc.dcd
! Do 1000000 steps at 298 K, writing energy 1000 steps.
! Grid-based insertions with 10 attempted orientations are used.
MC NSTEp 1000000 TEMPerature 298.0 ISEEd 302430 -
INBFrq -1 IECHeck 1000 IMGFrq -1 IUNC 32 NSAVc 1000 imall -
MUEX -5.8 DENS 0.03342 -
RGRId 0.25 GCCUt 2.5 NOTB 10 -
XMIN -12 YMIN -12 ZMIN -2.7 -
XMAX 12 YMAX 12 ZMAX 2.7
DELEte ATOM SELEct .BYRES. PROP X .GT. 9998.0 END
open write card unit 44 name gcmc.crd
write coor card unit 44 sele gcmc end
Could any one tell where the issue is?
Thank you.
I'm currently using Grand canonical monte carlo ensemble to simulate crystal water by inserting and deleting water atoms inside a crystal. The crystal.crd contains position of crystal atoms as well as H2O. crystal atoms are fixed and set inactive. I got an error of
MC E ENR: Eval# ENERgy Delta-E GRMS
MC E INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers
MC E EXTERN: VDWaals ELEC HBONds ASP USER
MC E IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec
MC E EWALD: EWKSum EWSElf EWEXcl EWQCor EWUTil
MC E PRESS: VIRE VIRI PRESSE PRESSI VOLUme
MC E LRCor: EVDW VIRI
---------- --------- --------- --------- --------- ---------
MC E> 0 28693807.808 0.000 39991243.434
MC E INTERN> 39.71400 71.43027 9.33503 125.67478 2.99950
MC E EXTERN> 157.74161 -227.80326 0.00000 0.00000 0.00000
MC E IMAGES> 28694837.626 -689.860 0.000 0.000 0.000
MC E EWALD> 43.99046 -3024.23481 2466.52214 0.00000 0.00000
MC E PRESS> -0.52165E+10 0.11479E+09 0.13065E+12 0.28750E+10 0.27377E+04
MC E LRCor> -5.32850 -10.65528
---------- --------- --------- --------- --------- ---------
***** LEVEL 2 WARNING FROM
***** REACHED GCMC LIMIT
******************************************
BOMLEV ( 0) IS NOT REACHED. WRNLEV IS 5
My scripts are like following:
*gcmc test simulation
*
!--- Read parameters, psf and coordinates
open read card name "top_all36_prot.rtf" unit 25
read rtf card unit 25
close unit 25
open read card name "par_all36m_prot.prm" unit 25
read parameter card unit 25 flex
close unit 25
stream toppar_water_ions.str
set cutnb 16.0 ! cutnb
set ctonnb 10.0 ! ctonnb
set ctofnb 12.0 ! ctofnb
set eatom atom
set etrun switch
set vatom vatom
set vtrun vswitch
OPEN UNIT 1 FORM READ NAME unit.psf
READ PSF CARD UNIT 1
CLOSe UNIT 1
! Read coordinates of starting structure
OPEN READ CARD UNIT 1 NAME crystal.crd
READ COOR CARD UNIT 1
CLOSE UNIT 1
!Set the active and blocking atoms
SCALar GCMC SET 0.0 SELEct IRES 1:12 END ! ires 1 to 12 is crystal
SCALar GCMC SET 1.0 SELEct IRES 13:42 END ! ires 13 to 42 is water
SCALar GCBLocker SET 1.0 SELEct all end
crystal define HEXAgonal 24.0709 24.0709 5.4560 90.00 90.00 120.00
crystal build noper 0 cutoff 30
update inbfrq -1 imgfrq -1 ihbfrq 0 imall -
ewald pmewald kappa 0.34 fftx 32 ffty 32 fftz 32 order 6 lrc -
@eatom @etrun @vatom @vtrun cutnb @cutnb ctonnb @ctonnb ctofnb @ctofnb -
cutim 999
ENERGY
! Create the MC move set
! Rigid translations
MOVE ADD MVTP RTRN BYREsidue WEIGht 1.0 DMAX 0.25 -
SELE (TYPE OH2) END LABEl DISP
! Rigid rotations
MOVE ADD MVTP RROT BYREsidue WEIGht 1.0 DMAX 30.0 -
SELE (TYPE OH2) END LABEl ROTA
! Insertion and deletion
MOVE ADD MVTP GCMC WEIGht 1.0 SELE (TYPE OH2) END LABEl GCMC
! Link the GCMC moves to the rotations and displacements to avoid moving
! inactive molecules.
MOVE LINK GCMC LAB1 GCMC LAB2 DISP
MOVE LINK GCMC LAB1 GCMC LAB2 ROTA
! Link the translations and rotations to each other for greater efficiency
MOVE LINK LAB1 DISP LAB2 ROTA
OPEN WRITE UNFOrmatted UNIT 32 NAME gcmc.dcd
! Do 1000000 steps at 298 K, writing energy 1000 steps.
! Grid-based insertions with 10 attempted orientations are used.
MC NSTEp 1000000 TEMPerature 298.0 ISEEd 302430 -
INBFrq -1 IECHeck 1000 IMGFrq -1 IUNC 32 NSAVc 1000 imall -
MUEX -5.8 DENS 0.03342 -
RGRId 0.25 GCCUt 2.5 NOTB 10 -
XMIN -12 YMIN -12 ZMIN -2.7 -
XMAX 12 YMAX 12 ZMAX 2.7
DELEte ATOM SELEct .BYRES. PROP X .GT. 9998.0 END
open write card unit 44 name gcmc.crd
write coor card unit 44 sele gcmc end
Could any one tell where the issue is?
Thank you.