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Trying to Perform NVT Dynamics
#37830 04/07/20 09:40 PM
Joined: Mar 2005
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rossi Offline OP
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Hello,

I have a problem with NVT dynamics. Something is going wrong, and I am not sure what I am doing incorrectly. At the end of the NVT run, the resulting pdb file has water molecules that are splay away from the RHDO crystl parameters that were provided. This is a simple system of solvated deca-alanine being prepared for a tutorial

! SETUP CRYSTAL (DEFINE, BUILD), IMAGE CENTERING W. MODIFIED PSF
! WE USE THE SAME PARAMS AS IN SOLVATION
set greaterval = 39.4379626 ! The actual value is read from the restart file
crystal define rhdo @greaterval @greaterval @greaterval 60. 90. 60.
crystal build noper 0

IMAGE BYSEG XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE SEGID HLX END
IMAGE BYRES XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE RESNAME TIP3 END
IMAGE BYRES XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE RESNAME SOD END
IMAGE BYRES XCEN 0.0 YCEN 0.0 ZCEN 0.0 SELE RESNAME CLA END

open unit 31 read card name /scratch/anr11010/charmm/alanine/ala10_alpha_helix_production-3.rst !restart file that will be read This file is derived from a fairly good equilibrated NPT dynamics run

! set up nonbond parameters -- same as for heating
nbond inbfrq -1 imgfrq -1 atom vatom cdie eps 1.0 -
elec ewald pmew fftx 48 ffty 48 fftz 48 kappa .34 spline order 6 -
vdw vswitch cutnb 16.0 cutim 16.0 ctofnb 12. ctonnb 10. wmin 1.0

calc pmass = ?stot * 0.02 ! from the tutorial in the text
calc tmass = stot * 0.20 ! from the tutorial in the text

calc pmass = int ( ?stot / 50.0 ) ! from the turorial
calc tmass = @pmass * 10 ! from the tutorial

! Constrain the hlx to center of simulation cell. ! It's a simple deca-alanine solvated and ions added according to the CHARMM tutorial
MMFP
GEO sphere RCM -
xref 0.0 yref 0.0 zref 0.0 -
force 10.0 droff 0.0 -
select segid hlx end
END

! set up shake
shake bonh param sele all end

! Dynamics Command
DYNA LEAP VERLET RESTRT CPT -
NSTEP 100000 TIMESTEP 0.001 -
IPRFRQ 1000 IHTFRQ 0 IEQFRQ 0 NTRFRQ 5000 -
IUNREA 31 IUNWRI -1 IUNCRD -1 IUNVEL -1 KUNIT -1 -
NPRINT 100 NSAVC 1000 NSAVV 0 ISVFRQ 1000 IHBFRQ 0 INBFRQ 25 -
HOOVER PCONS PMASS 0.0 PREF 1.0 REFT 300.0 TMASS @tmass PGAMMA 0 -
IASORS 0 IASVEL 1 ISCVEL 0 ICHECW 0 TWINDH 0.0 TWINDL 0.0 -
echeck 100.0

WHAT AM I DOING WRONG. THE ABOVE SCRIPT HAS BEEN MOSTLY GLEANED FROM THE CHARMM TUTORIAL PAGES.


As I stated above, the resulting structure is distorted after 100,000 steps. H2O molecules are flying away, although the output says the volume is constant. The pressure doesn't seem good. It's erratic.

Thanks so much for looking at this.

Kind regards,

Angelo

Re: Trying to Perform NVT Dynamics
rossi #37831 04/08/20 01:50 AM
Joined: Sep 2003
Posts: 8,447
rmv Online Content
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I see nothing obvious in the input; perhaps you've missed something in your careful reading of the output log file.

I generally start a new simulation when I switch ensembles.


Rick Venable
computational chemist


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