On 11/03/2015 06:11 PM, Jason Swails wrote:
> Moving this over to the developer's list
>
> On Tue, Nov 3, 2015 at 10:27 AM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
>>
>> OK. I got it now.
>> So, now, instead of 'restraint = coordinate(...)', I can do:
>> # d2-(d3-d4)
>> &rst iat = 11,48, 48, 49, 49, 16,
>> rstwt = 1,-1,1, r0 = 3.2, k0 = 0.0, /
>> and it works just fine.
>>
>
> ​Gerald -- am I correct in reading that this input works while the previous
> input with the "natural language" input did not?
Yes.
>
> If so, that raises a question as to what we should do here. Does anybody
> use this input option, and is anybody familiar with the code that can look
> into the issues and try to fix the bugs? If not, should we continue to
> keep natural language input around when fixes to the problem involve
> abandoning it altogether? (Does anybody use it on a regular basis?) Also,
> pmemd does not support this input (and likely never will), so these input
> files are sander-only.
>
> Thoughts?
Several things:
- I have not tested many things, but the problem I raised concerns the
use of the 'coordinate' keyword (in "restraint = coordinate(...)"). It
may/can/does work perfectly fine with other keywords.
- I can't find any examples of "restraint = coordinate(...)" in the
test/ and AmberTools/test/ directories. Moreover, the number of tests
using the restraint keyword is very limited (2-3 tests at most).
- The workaround that you suggested and that I now use (i.e., using
rstwt) works fine as long as one wants to restrain distances. If one
wants to restrain angles, planes, etc, that could be a potential problem.
- The fact that it is sander-only is, for me, not a problem since I use
it to do QM/MM umbrella sampling.
G.
>
> Thanks,
> Jason
>
--
____________________________________________________________________________
Prof. Gerald MONARD
SRSMC, Université de Lorraine, CNRS
Boulevard des Aiguillettes B.P. 70239
F-54506 Vandoeuvre-les-Nancy, FRANCE
e-mail : Gerald.Monard.univ-lorraine.fr
tel. : +33 (0)383.684.381
fax : +33 (0)383.684.371
web : http://www.monard.info
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Received on Tue Nov 03 2015 - 10:30:03 PST
