Hi

I've been trying to do some AXD runs, which require stopping and restarting to get around the time allowance on HPCs.

I've attached the starting input file (1tit_03_001_inp.txt), and the input file to restart the simulation (1tit_03_002_inp.txt). The second input works until the dynamics section when I get the following error:






CHARMM> DYNA CPT leap restart time 0.002 nstep @nstep -
CHARMM> nprint 1000 iprfrq 1000 ISVFRQ 10 ntrfrq 1000 -
CHARMM> iunread 11 iunwri 12 iuncrd 13 iunvel -1 kunit -1 -
CHARMM> nsavc 50000 nsavv 0 -
CHARMM> PCONSTANT pref 1.0 pmass @Pmass pgamma 20.0 -
CHARMM> HOOVER reft @temp tmass 2000.0 tbath @temp firstt @temp
Parameter: NSTEP -> "500000"
Parameter: PMASS -> "3583"
Parameter: TEMP -> "298"
Parameter: TEMP -> "298"
Parameter: TEMP -> "298"
IUNREA = 11 IUNWRI = 12 IUNOS = -1
IUNCRD = 13 IUNVEL = -1 KUNIT = -1
TITLE> * GENERATED BY CHARMM-GUI (HTTP://WWW.CHARMM-GUI.ORG) V2.0 ON JUN, 10. 2020. JOB
TITLE> * INPUT FILE FOR NPT DYNAMICS OF SOLVATED GLOBULAR PROTEIN
TITLE> * DATE: 7/20/20 15:36:18 CREATED BY USER: cm14sjm
TITLE> *

***** LEVEL 0 WARNING FROM *****
***** Crystal types do not match
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5








I've also tried including the following line from the starting input file:




!
! Image Setup
!

open read unit 10 card name ../../../crystal_image.str
CRYSTAL DEFINE @XTLtype @A @B @C @alpha @beta @gamma
CRYSTAL READ UNIT 10 CARD

!Image centering by residue
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele resname TIP3 end
IMAGE BYRESID XCEN @xcen YCEN @ycen ZCEN @zcen sele ( segid @posid .or. segid @negid ) end

!
! Nonbonded Options
!

nbonds atom vatom vfswitch bycb -
ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 -
inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6
energy

!
!use a restraint to place center of mass of the molecules near the origin
!

MMFP
GEO rcm sphere -
Xref @xcen Yref @ycen Zref @zcen XDIR 1.0 YDIR 1.0 ZDIR 1.0 -
harmonic FORCE 1.0 select .not. ( hydrogen .or. resname TIP3 .or. segid @posid .or. segid @negid ) end
END





But this gives me this error instead:







CHARMM> nbonds atom vatom vfswitch bycb -
CHARMM> ctonnb 10.0 ctofnb 12.0 cutnb 16.0 cutim 16.0 -
CHARMM> inbfrq -1 imgfrq -1 wmin 1.0 cdie eps 1.0 -
CHARMM> ewald pmew fftx @fftx ffty @ffty fftz @fftz kappa .34 spline order 6
Parameter: FFTX -> "80"
Parameter: FFTY -> "80"
Parameter: FFTZ -> "80"

***** LEVEL -1 WARNING FROM *****
***** SOME ATOM COORDINATES UNDEFINED OR OUT OF RANGE
******************************************
BOMLEV ( 0) IS REACHED - TERMINATING. WRNLEV IS 5


Does anybody know what I'm doing wrong?

Thank you

Attached Files
1tit_03_001_inp.txt (4.37 KB, 17 downloads)
SHA1: 021d9b99134758e975619b1c70893553dee805f6
1tit_03_002_inp.txt (3.43 KB, 17 downloads)
SHA1: be5618d619eb5626bf8e2771d39fab43a9c8ec84