Re: Kb, Ktheta values for TIP3P water model

From: Kenno Vanommeslaeghe (
Date: Sun Aug 10 2014 - 17:49:01 CDT

On 08/07/2014 06:15 PM, Hadi wrote:
> except encouraging you to develop some force field in
> NAMD with rigidBonds all option.

That would be the CHARMM force field, as explained earlier.

> Again, I am sorry you misunderstood my statements. Your recent email
> clearly shows that you were not aware of force constant problem until very
> recently in this thread although it was the first response in the thread.

There in no "force constants problem" in the sense you've been claiming,
just an exception rule (see below).

Either way, I'm glad you noticed I'm trying to have a mature discussion by
being honest and transparent. I could easily have made up an excuse (like
"you misunderstood me") to make it look like I knew this all along, just
like you're trying to make it look like you knew about rigidBonds when you
first replied to Viswanath's e-mail and understand what it does...

> In contrast to your claim, I believe there are more complexities

Since you're a programmer, can you make an educated guess what the below
extract from the NAMD source (Molecule.C) does?

If Viswanath would have noticed that warning and included it in his
original question, everything would have been clear and we wouldn't been
having this endless discussion. Did you notice it when trying to reproduce
his problem?

   /* Loop through and read in all the bonds */
   while (num_read < numBonds)
     if (simParams->lonepairs) {
     else {
       if ( k == 0. ) --numBonds; // fake bond
       else ++num_read; // real bond

   /* Tell user about our subterfuge */
   if ( numBonds != origNumBonds ) {
     iout << iWARN << "Ignored " << origNumBonds - numBonds <<
             " bonds with zero force constants.\n" << endi;

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