I dealt with this problem a couple of days ago in mdgx and had to fix the
zeros by intercepting them as I populated the list of the scaling factors
actually implemented in the calculation. I make a list of "adjustment"
factors for 1-4 scaling terms, which are basically 1 - 1.0/T where T is
the 1-4 term read in from the topology. When T is zero I make T=1.0, so
that the adjustment term comes out to be zero and the overall effect is
that the 1-4 interaction is unchanged. So, as far as I'm concerned I have
dealt with this issue. But, it would seem simpler to designate "1.0" in
the topology where a 1-4 bonded term is not meant to be scaled.
Dave
> Hi Jason,
>
>> I have a slight concern regarding variable 1-4 scaling as it's
>> implemented
>> in tleap. Looking at one of the topology files created by tleap, it
>> appears
>> as though several dihedral 1-4 scaling parameters are just set to 0 in
>> the
>> topology file. However, it also appears these may correspond to
>> ignored
>> scaling factors (as with multi-term dihedrals and impropers, etc.), so
>> they
>> don't really affect results (hopefully). Indeed in a small test case,
>> hard-coding all of the 1-4 scaling constants to be 1.2 and 2.0 appears
>> to
>> leave the results unchanged wrt the old topology file.
>>
>> They are inverted as soon as they're read in, though, so "0" may not be
>> the
>> most industrious of choices here... Is there something I'm missing?
>
> This was my suggestion and adding the 0 to ignored dihedrals knowing it
> would be inverted was the whole point. That way if anything is messed up
> in
> the code for calculating the 1-4 scaling or something modifies the list in
> a
> correct way you will end up with infinite energies and forces for the 1-4
> EEL and VDW terms and the calculation should stop. Rather than producing
> 'slightly' wrong results.
>
> It also makes it easier to see which dihedrals are duplicates or not.
>
> I guess the only issue is if a compiler objects to a division by zero but
> my
> understanding is that division by a floating zero should not throw and
> error, only integer division by zero should do this.
>
> All the best
> Ross
>
>
> /\
> \/
> |\oss Walker
>
> ---------------------------------------------------------
> | Assistant Research Professor |
> | San Diego Supercomputer Center |
> | Adjunct Assistant Professor |
> | Dept. of Chemistry and Biochemistry |
> | University of California San Diego |
> | NVIDIA Fellow |
> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
> ---------------------------------------------------------
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
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Received on Fri Aug 12 2011 - 11:00:03 PDT
