From: Viswanath Pasumarthi (v.pasumarthi_at_iitg.ernet.in)
Date: Wed Aug 13 2014 - 02:27:24 CDT
> In NAMD, 1 rigid water molecule adds "2" to "Info: * BONDS", and "3" to
> "Info: * RIGID BONDS". So, NAMD simulations of 200 rigid water molecules
> should report 200 angles (Info: * Angles), 400 bonds (Info: * Bonds), and
> 600 rigid bonds (Info: * rigid bonds). In this respect, seeing 600 rigid
> bonds for 200 water molecules in NAMD log is fine.
> Did you notice that your system is not neutral? This is not great.
>> TOTAL CHARGE = 18.0571 e
The polarity of atomic charges for some specific atoms were wrongly
assigned. This is my mistake, thanks for pointing this out.
> Perhaps, it would be better to rebuild your system. You can explicitly
> remove (or comment out) hydrogen-hydrogen bond from your topology file.
> Another question: can you find the following lines in your log file?
> Info: RIGID BONDS TO HYDROGEN : ALL
> Info: ERROR TOLERANCE : 1e-08
> Info: MAX ITERATIONS : 100
> Info: RIGID WATER USING SETTLE ALGORITHM
yes, they are present.
> On Aug 12, 2014, at 12:19 PM, Viswanath Pasumarthi
> <v.pasumarthi_at_iitg.ernet.in> wrote:
>> 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
>> bond with force constants, kb = 1,2,5,10,100,450, the bond lengths
>> 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
>> rigid molecule.
>> 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
>> 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
>> 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
>> !TIP3P WATER
>> OW HT 450.0000 0.9572 !
>> !atom types Ktheta Theta0 Kub S0
>> !TIP3P Water
>> HT OW HT 55.0000 104.52 !
>> !atom ignored epsilon Rmin/2 ignored eps,1-4
>> !TIP3P Water
>> 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
>>>> 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
>>>> (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
>>> simulations behave correctly for all force constants (even absurd
>>> 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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