# Re: [AMBER] &rst + distance + coordinate restraint

From: Gerald Monard <Gerald.Monard.univ-lorraine.fr>
Date: Tue, 3 Nov 2015 15:39:32 +0100

Hello,

On 11/01/2015 11:52 AM, Jason Swails wrote:
> On Sat, Oct 31, 2015 at 1:21 PM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
>> As a follow-up, I can partially solve the problem using "iat":
>> # d2
>> &rst iat = 11, 48, r0 = 3.2, k0 = 0., /
>> # d3
>> &rst iat = 48, 49, r0 = 3.2, k0 = 0., /
>> # d4
>> &rst iat = 49, 16, r0 = 3.2, k0 = 0., /
>> # d2-(d3-d4)
>> &rst restraint = "coordinate(distance( :1.C :3.O ), 1.0, distance(
>> :3.O :3.H1 ), -1.0, distance( :3.H1 :2.OP2 ), 1.0 )", r0 = 3.2, k0 =
>> 0., /
>>
>
> ​What happens if you use the "iat" approach here as well? I've often
> observed rather funny behavior with the "natural language" restraints, and
> there are a number of peculiar things about that code (for instance -- it
> doesn't use the standard mask parser, it implements its own highly limited
> version).
>
> ​​

Well, the problem is that I want to use the 'coordinate' mode because I
want to restrain the difference between 2 distances. I don't see how to
do that with iat.
I tried the 'igr' command also (it is mentionned in the manual an
unclear relationship between the two), but with no success.
Thus I've started to check the code...

For the moment, because my reaction coordinate is a distance vs. the
difference of 2 distances (2D PES), I can manage to run the systems with
my solution above. But I cannot combine 'restraint' keywords that uses
'coordinate' definitions.

G.

>> But I still can't add multiple "&rst restraint=[...]" commands.
>> ​​
>> I haven't seen such restriction in the manual, but may be I haven't
>> ​​
>> search correctly.
>>
>
> ​There shouldn't be such a restriction, but I don't know that the code is
> that well-tested (and it's quite complex as well).
>
> All the best,
> Jason
>

```--
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Received on Tue Nov 03 2015 - 07:00:03 PST
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