[gmx-users] Constraints of distance

[Dr. Vitaly Chaban]

Steven -

I probably know nothing about "function #2", but "function 1" is used just
everywhere. It does constrain intramolecular distances.

Good luck. Vitaly


Dr. Vitaly Chaban


On Tue, Jun 11, 2013 at 4:46 PM, Steven Neumann <s.neumann08 at gmail.com>wrote:

> I was not sure about the fucntion type (1 or 2). Once in manual it is
> stated that function 1 is only for exclusions and another time it can be
> used to miimc bonds. Both functions are working though.  Thanks anyway.
>
> Steven
>
>
> On Tue, Jun 11, 2013 at 2:18 PM, Dr. Vitaly Chaban <vvchaban at gmail.com>wrote:
>
>> I think all is correct.
>>
>> Why are you asking? People normally report problems.
>>
>> Dr. Vitaly Chaban
>>
>>
>>
>>
>>
>>
>> On Tue, Jun 11, 2013 at 12:30 PM, Steven Neumann <s.neumann08 at gmail.com
>> >wrote:
>>
>> > Dear Gmx Users,
>> >
>> > I am running CG simulation and I wish my beads to be constraint - one
>> away
>> > from each other of 0.4 nm. I wan to use Lincs for this purpose. I do not
>> > have any bonds in my topology or rtp entry. I just add:
>> >
>> > [ constraints ]
>> > 1     2      1      0.4
>> > 2     3      1      0.4
>> > ...
>> > 31   32     1      0.4
>> >
>> > constraints = none
>> > constraint_algorithm     = Lincs
>> >
>> >
>> > Is that correct? I used function 1, is that right?
>> >
>> > Shall I specify something else?
>> >
>> >
>> > Steven
>> > --
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>
>