From: Hadi (dinpajooh_at_gmail.com)
Date: Sun Aug 10 2014 - 20:59:58 CDT
On Sun, Aug 10, 2014 at 3:49 PM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:
> 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.
>
>
Not necessarily. One can develop a force field that is not a CHARMM force
field in a more general physics problem.
>
> 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?
>
Molecule.C checks the force constant values and sends a warning message if
the force constant is zero. However, NAMD is a program which consists of
thousands of lines, and the algorithms that use bond constraints have their
own limitations. I am not sure how NAMD addressed those issues about bond
constraints. Even when the rigid model can be defined by bond constraints,
the network of bonds produced may be problematic. Molecule.C is just one
subroutine that may or may not be related to the problems.
> 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?
>
I had a similar experience before I responded to the first e-mail, but I
was not sure if this was the cause of the problem.
> /* Loop through and read in all the bonds */
> while (num_read < numBonds)
> {
> -snip-
> if (simParams->lonepairs) {
> -snip-
> 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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