If that is the only difference in the entire test, then it is probably
not a big deal. It appears as though someone has changed the
restraint inputs for the test.
It is advisable to use larger restraint gap between R1 and R2 in
general, as the biassing potential becomes linear past R1 (so it is no
longer harmonic). However, if the system never migrates more than 15
degrees past the restrained dihedral, then the biassing potential will
look no different throughout the simulation (and that is likely the
case with such a strong force constant).
I would check to see if the input in that test case sets R1 to 0, just
to make sure that it was not accidentally hard-coded into the code (in
which case that would need to be fixed).
Thanks!
Jason
On Mon, Jan 25, 2010 at 10:22 AM, Hopkins, Robert <hopkins.uhcl.edu> wrote:
> Dear Amber Users,
>
> I recently re-installed Amber 10 with all of the current bugfixes, in a Cygwin environment. Nearly all the tests passed, exept for the following (for $AMBERHOME/test/jar/mdout.jar.dif):
>
> < R1 = -85.000 R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000
>
> ---
>
>> R1 = 0. R2 = 15.000 R3 = 15.000 R4 = 115.000 RK2 =5000.000 RK3 = 5000.000
>
> Note that the two values for R1 are significantly different. Is this a difference that should concern me? Thanks for any comments or suggestions.
>
> Bob Hopkins
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Mon Jan 25 2010 - 08:30:03 PST
