Hey guys,
Thanks Jason for the thorough reference. I am currently comparing 2 prmtop
files, and their LENNARD_JONES_ACOEFF (& ...BCOEFF) sections are almost
identical with a few discrepancies. In your reference, you comment that
there are [NTYPES X (NTYPES + 1)] / 2 entries. Could you explain why there
are this many entries and how to know which pair of atoms corresponds to
which entry?
Thanks,
David Winogradoff
On Thu, May 16, 2013 at 9:07 AM, David Winogradoff <dwino218.gmail.com>wrote:
> Thanks for the info and link.
>
>
> On Wed, May 15, 2013 at 7:18 PM, Jason Swails <jason.swails.gmail.com>wrote:
>
>> I had put together a prmtop reference for myself recently. It's attached
>> here in the hopes it will be helpful. (It's an appendix from my
>> dissertation ripped out of context and re-compiled as a standalone tex
>> document, so there may be errors). The website Hai pointed you to probably
>> has enough information, but I think my document is a little bit more
>> thorough.
>>
>> HTH,
>> Jason
>>
>>
>> On Wed, May 15, 2013 at 5:13 PM, David Winogradoff <dwino218.gmail.com
>> >wrote:
>>
>> > There are several flags within the prmtop files that I understand, but I
>> > would like to gain a better understanding of the Lennard Jones
>> coefficient
>> > flags.
>> >
>> > After the following lines:
>> >
>> > %FLAG LENNARD_JONES_ACOEF
>> > %FORMAT(5E16.8)
>> >
>> > there appears to be a matrix of numbers, which I'm guessing is an n x n
>> > matrix put into a 5-column format. I am also guessing n is the number of
>> > unique atom-types present. Beyond these guesses, I do not know.
>> >
>> > Could someone provide an explanation for how to interpret these flags,
>> or
>> > provide a link where an explanation may be found?
>> >
>> > Thanks,
>> > David Winogradoff
>> > ~~~~~~~~~~~~~~~~~
>> > Graduate Student
>> > University of Maryland
>> > College Park
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Jason M. Swails
>> Quantum Theory Project,
>> University of Florida
>> Ph.D. Candidate
>> 352-392-4032
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>>
>
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Received on Thu May 16 2013 - 09:00:04 PDT
