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large negative pressures??
#1295 04/22/04 09:23 PM
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I am having a lot of trouble with anomolous pressure calculations in
charmm (huge positive and negative pressures, i.e. -30000 atm). I tried
using DYNA CPT to alleviate this problem, but it didn't help. Here are two examples:

Any insight you could provide would be much appreciated,

Jim Sullivan



CHARMM> Dynamics cpt -
CHARMM> leap STRT NSTEP 2500 TIMESTEP 0.00050 -
CHARMM> inbfrq -1 ihbfrq 0 ilbfrq 0 -
CHARMM> IUNCRD -1 IUNVEL -1 KUNIT 50 IUNWRI -1 IUNREA -1 -
CHARMM> IPRFRQ 100 NPRINT 250 NSAVC 0 NSAVV 0 -
CHARMM> IASORS 1 IASVEL 1 NTRFRQ 1500 -
CHARMM> FIRSTT 12.0 FINALT @cooltemp TEMINC 12.0 -
CHARMM> IHTFRQ 50 IEQFRQ 0 ICHECKW 0 TWINDH 10.0 TWINDL -10.0 -
CHARMM> cutim @look cutnb @look ctonnb @on ctofnb @off switch vswitch -
CHARMM> !ewald pmewald kappa @kap fftx @2 ffty @3 fftz @4 order 6 -
CHARMM> ISEED 314159 -
CHARMM> !kappa between 4/cutoff & 5/cutoff
CHARMM> pconstant pmass 100.0 pmzz 1.0 pmyy 0.0 pmxx 0.0 pgamma 20.0

DETAILS ABOUT CENTRE OF MASS
POSITION : 8.92996199E-02 4.15338700E-02 0.24337901
VELOCITY : -5.17022197E-05 2.02991079E-04
2.61798625E-04
ANGULAR MOMENTUM : -67.585059 -4597.6989 3124.3912
KINETIC ENERGY : 1.78159603E-02
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 PRESS: VIRE VIRI PRESSE PRESSI
VOLUme
---------- --------- --------- --------- ---------
---------
DYNA> 0 0.00000-386171.94471 1900.77166-388072.71637
15.04801
DYNA PROP> 66.65932-385396.93136 4225.81172
775.01336*************
DYNA INTERN> 6374.47606 5771.21635 631.75555 3693.14970
15.90898
DYNA EXTERN> 37021.42128-402078.57220 0.00000 0.00000
0.00000
DYNA IMAGES> 1933.43256 -41435.50465 0.00000 0.00000
0.00000
DYNA PRESS> *************2284166.96383 281957.65638 399135.50615
392885.43720
---------- --------- --------- --------- ---------
---------
Crystal Parameters : Crystal Type = ORTH
DYNA A = 39.95890 B = 40.37300 C = 243.53500
DYNA Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000
DYNA PIXX = 407744.41 PIYY = 360218.80 PIZZ = 429443.31
DYNA PIXY = -10172.89 PIXZ = -50367.39 PIYZ = -8033.74
DYNA Gradient Norm = **********

UPDECI: Nonbond update at step 1
UPDECI: Nonbond update at step 2
TOTAL ENERGY CHANGE EXCEEDED
20. KCAL AND 10% OF THE TOTAL KINETIC ENERGY IN THE LAST STEP
PREVIOUS E = -0.4075E+06 CURRENT E = -0.4198E+06 KINETIC =
0.7611E+05



Dynamics -
CHARMM> leap STRT NSTEP 2500 TIMESTEP 0.0010 -
CHARMM> inbfrq -1 ihbfrq 0 ilbfrq 0 -
CHARMM> IUNCRD -1 IUNVEL -1 KUNIT 50 IUNWRI -1 IUNREA -1 -
CHARMM> IPRFRQ 100 NPRINT 250 NSAVC 0 NSAVV 0 -
CHARMM> IASORS 1 IASVEL 1 NTRFRQ 1500 -
CHARMM> FIRSTT 12.0 FINALT @cooltemp TEMINC 12.0 -
CHARMM> IHTFRQ 50 IEQFRQ 0 ICHECKW 0 TWINDH 10.0 TWINDL -10.0 -
CHARMM> cutim @look cutnb @look ctonnb @on ctofnb @off switch vswitch
-
CHARMM> ISEED 314159



DETAILS ABOUT CENTRE OF MASS
POSITION : 3.97654140E-02 5.25810953E-02 0.16618615
VELOCITY : -1.56776257E-04 -2.36864462E-03
-1.94037615E-05
ANGULAR MOMENTUM : 9447.1898 23395.556 -547.88572
KINETIC ENERGY : 0.89310894
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 PRESS: VIRE VIRI PRESSE PRESSI
VOLUme
---------- --------- --------- --------- ---------
---------
DYNA> 600 0.60000************* 19677.37121*************
155.78163
DYNA PROP> 20.35458************* 20766.51179 363.04686
24433.48843
DYNA INTERN> 101712.00064 53379.25232 1172.99463 5467.18164
449.15768
DYNA EXTERN> 114391.57333************* 0.00000 0.00000
0.00000
DYNA IMAGES> 6956.66557-776352.69310 0.00000 0.00000
0.00000
DYNA PRESS> 155654.46481-171943.45710 -27165.56781 -27592.22011
392885.43720
---------- --------- --------- --------- ---------
---------


Molecular Engineering Laboratory University of Washington
Re: large negative pressures??
jimpsull #1296 04/22/04 10:11 PM
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For the CPT dynamics, you should specify either PMASS or the 3 anisotropic terms PMXX, PMYY, and PMZZ, but not both. You also need to specify PREF, the target pressure.

A large negative pressure indicates that the system would like to shrink, and bring the molecules closer together.

Trouble with starting up a dynamics run often means the initial model may be problematic, and may need some additional minimization at the least. I've found it to be fairly important to minimize under the same conditions (nonbond, images, SHAKE, etc.) as will be used for the dynamics.



Rick Venable
computational chemist

Negative pressures
rmv #1297 04/23/04 10:02 PM
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Thank you very much. I do still have one question. One of the reasons that I'm using CPT is to fix the volume which is arbitrary after I've built my system. That is, after I've added my DNA and ions & deleted overlapping waters the system density is probably not correct. If I define my PBC before minimization, how will longer minimization fix my pressure issues? Is it possible to use CPT for minimization?:

crystal free
crystal define orth @7 @9 @zl 90.0 90.0 90.0
crystal build noper 0 cutoff @off
image byresidue xcen @xspot ycen @yspot zcen @zspot sele all end

Thanks again,

Jim Sullivan


Molecular Engineering Laboratory University of Washington
HUGE pressure fluctuations (was: large negative...
rmv #1298 04/26/04 05:51 AM
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Just a follow-up to the previous question: doing a MD with cubic PBC (side of the cube ~70 A) and constant pressure conditions defined like this

hoover tmass 1000 reft 300.0 -
pconst pint pref 1.0 pmass 500.0 pgamma 20.0 tbath 300.0

I always see pressure fluctuations as huge as 500-1000 atm. approximately around my reference pressure of 1 atm:

AVER PRESS> 4258.81513 -16492.70012 -1114.26439 35.35039 262056.21531

FLUC PRESS> 2196.04327 1483.55976 573.77782 388.32338 500.28536

I understand that the system is very small by macroscopic standards and I couldn't expect the true constant pressure in it. But are such big fluctuations normal?

Thanks,

Michael

Re: Negative pressures
jimpsull #1299 04/26/04 07:31 PM
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The pressure is computed using the forces, so improved minimization leading to a lower potential energy (substantially negative) can directly affect the initial pressure.

By not minimizing using the same conditions, there can be a large potential change in going from a minimized model to the zeroth and first dynamics steps.

Assuming CRYSTAL is setup, you can easily compute the density:

! CONVERTS amu/A**3 to g/cc
set amu = 1.665
! ASSUMES, ORTH, TETR, or CUBIC; SEE crystl.doc FOR OTHER SHAPES
calc vol = ?XTLA * ?XTLB * ?XTLC
! PUTS TOTAL MASS INTO ?STOT
scalar mass stat
! COMPUTE DENSITY IN GM/CC
calc rho = @AMU * ?STOT / @VOL

It is possible to use the LATTICE keyword during minimization with the ABNR algorithm, but it may be better to adjust your initial unit cell edges manually, based on the pressure. Note that one can estimate the pressure after minimization, via something like

presssure init
mini ...
pressure inst temp 298. volu @VOL

assuming that VOL was computed as for the density.




Rick Venable
computational chemist

Re: HUGE pressure fluctuations (was: large negativ
mishapopov #1300 04/26/04 07:35 PM
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Pressure fluctuations of 100s of atm are completely normal.



Rick Venable
computational chemist


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