From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Tue Aug 12 2014 - 12:19:00 CDT
Yes Kenno, there is a warning message which I have failed to notice when
force constant values for O-H bond and H-O-H angle are taken to be zero.
Warning: Ignored 400 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
Warning: Ignored 200 angles with zero force constants.
Moving on, as Maxim suggested, on checking the variation of length of O-H
bond with force constants, kb = 1,2,5,10,100,450, the bond lengths varied
from 5% to 15% on average for 10 randomly selected bonds. This only
reinforces the failure of rigidBonds all constraint. But the second
warning message posted above indicates that NAMD identified water as a
The following is an excerpt from output log file for a system involving
ionic liquid+water mixture. 20 IL molecules + 200 H2O molecules were
considered. It can be seen that 900 rigid bonds are identified. Each IL
molecule contains 15 covalent bonds involving hydrogen, which makes 300
rigid bonds corresponding to IL. The rest 600, contributes from 200 water
molecules, which implies even H-H is considered as an explicit bond for
water molecule. Is it alright and does it mean the bond parameters for H-H
should also be provided?
Info: STRUCTURE SUMMARY:
Info: 1400 ATOMS
Info: 1180 BONDS
Info: 1600 ANGLES
Info: 1660 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 0 EXCLUSIONS
Info: 900 RIGID BONDS
Info: 3297 DEGREES OF FREEDOM
Info: 700 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 700 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 11990.3 amu
Info: TOTAL CHARGE = 18.0571 e
Info: MASS DENSITY = 0.73744 g/cm^3
Info: ATOM DENSITY = 0.0518519 atoms/A^3
801 MOL 1 UNK O OW -0.928231 15.9994 0
802 MOL 1 UNK H HT 0.464116 1.00794 0
803 MOL 1 UNK H HT 0.464116 1.00794 0
!atom type Kb b0
OW HT 450.0000 0.9572 !
!atom types Ktheta Theta0 Kub S0
HT OW HT 55.0000 104.52 !
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
HT 0.000000 -0.046000 0.224500 !
OW 0.000000 -0.152100 1.768200 !
> On 08/11/2014 01:56 PM, Viswanath Pasumarthi wrote:
>> considering a value of k=0 mean absence of spring (physical
>> bond) between the respective atoms. It would have been easier to
>> understand this mistake had there been an error message pointing to the
>> choice of k value as zero.
> But there *is* a message, and if you would have noticed/posted it, we
> wouldn't have needed to have this long, marginally constructive
> discussion. Look in your NAMD output for the following:
> Warning: Ignored .* bonds with zero force constants.
> Warning: Ignored .* angles with zero force constants.
> Where .* is an integer.
>> However, using rigidBonds constraints still
>> required bond constraint values to be specified in the parameter file.
>> This, as Kenno cautioned has turned into a flexible simulation, as
>> covalent bonds involving hydrogen became more flexible at lower k values
>> (1,2,5,10) and functioning decent at the values reported in modified
> I have to repeat that I tried and failed to reproduce this; my rigidBonds
> simulations behave correctly for all force constants (even absurd values
> such as 0.0001 or -10000) except zero. Most probably, there is an issue
> with your psf and/or rigidBonds is not applied correctly. Which I have
> been saying from the very beginning!
> You probably need to try to use more detailed language (for example
> "distances" or "force constants" rather than "values") when describing
> your problem, and attach relevant input and output files to your posts,
> else we'll never get anywhere.
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