Previous Thread
Next Thread
Print Thread
minimization of LATTice
#36945 04/25/18 01:36 PM
Joined: Oct 2017
Posts: 38
R
Rohit Offline OP
Forum Member
OP Offline
Forum Member
R
Joined: Oct 2017
Posts: 38
Hi,

my system is 50*50*50 cube water+urea+protein.

after normal mini sd and ABNR my box size changes to 52*53*53
is there any way to get this box size and continue with dynamics. below is my script

Code:
!================================================================
! Minimize after solvation
!================================================================
!MINI SD NSTEP 100
!MINI SD NSTEP LATTice
MINI ABNR LATTice NSTEP 500
calc vol = ?XTLA * ?XTLB * ?XTLC
!================================================================
! Write psf, crd and pdb file
!================================================================
WRITE PSF  CARD NAME "./eqf10/pu8_min.psf"
* PSF
*

WRITE COOR CARD NAME "./eqf10/pu8_min.crd"
* CRD
*

WRITE COOR PDB NAME "./eqf10/pu8_min.pdb"
* PDB
*

!================================================================
! Heat the system
!================================================================
OPEN WRITE UNIT 31 CARD NAME "./eqf10/pu8_heq.res"      ! Restart file
OPEN WRITE UNIT 32 FILE NAME "./eqf10/pu8_heq.dcd"      ! Coordinates file

define backbone sele (type N .or. type CA .or. type C) .and. segid PRT end
cons harm absolute FORCE 10.0 MASS sele backbone end

dyna cpt start nstep 100000 timestep 0.001      -
    pcons pint pref 1.0 pmass @PMASS pgamma 25. -
    INBFRQ -1 IMGFRQ -1                         -
    nprint 100 iprfrq 5000 ihtfrq 1000 ieqfrq 1000 ntrfrq 1000 -
    firstt  60.00 finalt 360.00 teminc 10.0  tbath 360.00 -
    iasors 1 iasvel 1 iscvel 0 ichecw 1 twindh 5.0 twindl -5.0 -
    IUNWRITE 31 IUNCRD 32 NSAVC 1000

cons harm clear

Re: minimization of LATTice
Rohit #36946 04/25/18 05:48 PM
Joined: Sep 2003
Posts: 8,450
rmv Online Content
Forum Member
Online Content
Forum Member
Joined: Sep 2003
Posts: 8,450
If you want the system to remain cubic (and you probably should), use the CUBIC lattice type for the CRYSTAL setup. Then the edge lengths are constrained such that a=b=c; otherwise, they are free to change.


Rick Venable
computational chemist


Moderated by  BRBrooks, John Legato 

Link Copied to Clipboard
Powered by UBB.threads™ PHP Forum Software 7.7.4
(Release build 20200307)
Responsive Width:

PHP: 5.6.33-0+deb8u1 Page Time: 0.008s Queries: 18 (0.004s) Memory: 0.8932 MB (Peak: 0.9573 MB) Data Comp: Off Server Time: 2020-06-03 19:59:09 UTC
Valid HTML 5 and Valid CSS