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#37163 - 09/26/18 01:52 AM Re: Pressure unit in charmm [Re: Giselle]
vidhya Offline
Forum Member

Registered: 08/09/18
Posts: 10
Loc: India
Hi

I performed the MD run using Langevin dynamics as given in the CHARMM tutorial.
I am able to run the simulation without any issues in temperature control. My only concern is the pressure.
The log file shows that the pressure is O atm.
This means the simulation is running as such it is in vacuum.

I have given the scalar fbeta to be 5 ps-1 as per the reference paper given in mmfp.doc.
From what I read, LD is mostly used for implicit solvent simulations. And we do not define the pressure but still LD says it runs in NPT ensemble.

Here is a sample of my output:
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 MMFP: GEO MDIP SSBP SHEL DROFfa
DYNA PRESS: VIRE VIRI PRESSE PRESSI VOLUme
DYNA UMBR: ADUMB RXNCor GAMUS
---------- --------- --------- --------- --------- ---------
DYNA> 2000 4.00000 -1630.14038 808.23955 -2438.37994 307.77499
DYNA PROP> 21.74849 -1585.83007 937.07987 44.31031 1170.23642
DYNA INTERN> 394.96040 168.31806 0.00000 0.00000 0.00000
DYNA EXTERN> 425.32588 -3617.00872 0.00000 0.00000 0.00000
DYNA IMAGES> 0.00000 0.00000 0.00000 0.00000 0.62431
DYNA MMFP> 0.20326 0.00000 189.03856 0.00000 0.00000
DYNA PRESS> -18.12466 -762.03295 0.00000 0.00000 0.00000
DYNA UMBR> 0.00000 0.15832 0.00000
---------- --------- --------- --------- --------- ---------

My pressure is 0 throughout the simulation.
How can I set the pressure constant to be around 1 atm?

Input file:
!Defining spherical solvent boundary potential
MMFP
SSBP SELE TYPE OH2 END
GEO sphere RCM -
xref 0.0 yref 0.0 zref 0.0 -
force 10.0 droff 0.0 -
select segid PI .or. segid NI end
END

CONS HARM BESTFIT MASS FORCE 10.0 SELE SEGId PI END NOROT
CONS HARM BESTFIT MASS FORCE 10.0 SELE SEGId NI END NOROT

!Initialized Langevin dynamics
SCALAR FBETA SET 5.0 SELEct TYPE OH2 .AND. SEGId W END

!Defining non-bonded interactions
NBONDS GROUP SWITCH CDIE VDW VSWI EXTEND GRAD QUAD -
CUTNB 22.0 CTOFNB 20.0 CTONNB 18.0 WMIN 1.5 EPS 1.0

!Adaptive umbrella sampling for distance
rxncor: define set1 point sele atom PI 1 SOD end
rxncor: define set2 point sele atom NI 1 CLA end
rxncor: define rc distance set1 set2
rxncor: set rc
rxncor: trace rc unit 31
rxncor: UMBRella name rc KUMB @kumb DEL0 @del0 FORM 1
calc lowdel = @del0 - 1.5
calc hidel = @del0 + 1.5
rxncor: statistics name rc lowdelta @lowdel hidelta @hidel deldel 0.05 start 500

!Heating the system using thermostat
OPEN READ FORMatted UNIT 21 NAME @equ.res
OPEN WRITe FORMatted UNIT 20 NAME @umb.res
OPEN WRITe UNFOrmatted UNIT 22 NAME @umb.dcd

DYNA LEAP LANGEVIN STARt -
NSTEP 150000 TIMESTep 0.002 NPRINT 1000 -
FIRSTT 300.0 FINALT 300.0 TBATH 300.0 IHTFRQ 0 TWINDH 5.0 TWINDL -5.0 -
IUNREAd -1 IUNWRIte 20 IUNCRD 22 NSAVC 50 -
IEQFRQ 0 IPRFRQ 1000 NTRFRQ 1000 INBFRQ -1 IMGFRQ -1 -
IASORS 1 IASVEL 1 ISCVEL 0 ICHECW 1 ECHECK 2000

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#37164 - 09/26/18 10:29 AM Re: Pressure unit in charmm [Re: Giselle]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8259
Loc: 39 03 48 N, 77 06 54 W
The output also shows a volume of zero; the pressure cannot be computed w/o a defined volume. The simulation pressure codes in CHARMM require the use of periodic boundary conditions.

You may be able to get a crude estimate of the pressure in an ad hoc way, before or after a simulation, using the PRESS INST command and supplying a volume and temperature. Estimating the volume of your droplet may be challenging. You may wish to research the topic of computing pressure in a droplet.

You could also try contacting the SSBP code authors.
_________________________
Rick Venable
computational chemist


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