[gmx-users] constranit distance for pulling code

[Justin A. Lemkul]

On 5/16/12 6:50 PM, xiaowu759 wrote:
> Dear gmxers,
> I have prepared the inputs and tried to run constraint distance pulling on
> two-molecule pair. However, one error is output which indicates that two atoms
> on the molecule including the pull group are beyond the 1-4 table range. I have

I'm assuming you're seeing something like:

http://www.gromacs.org/Documentation/Errors#1-4_interaction_not_within_cut-offhttp://www.gromacs.org/Documentation/Errors#LINCS.2fSETTLE.2fSHAKE_warnings

Please always copy and paste the exact error message.

> chosen one reference group and one pull group. And both groups are parts of
> whole molecules. I find that no error is given when only pull opinions are
> commented out. So I guess this error can be caused by the pull code, i.e., the
> pull group is suddently moved to the distance defined by pull_init1, but the
> rest of molecule is not moved a bit, which leads to one much bigger 1-4
> distance. Is it right? Cannot the pull code deal with the two groups belonging
> to only parts of two molecules? Please give me some hints, thanks a lot.

The problem is that you're asking the pull code to do something that is 
physically unreasonable.  Your assessment regarding the pull_init1 value is 
correct - you're asking the pull code to immediate constrain the intramolecular 
distance to some target, and it cannot do it.  If you wish to pull the molecule 
apart (as in unfolding a protein), you'll have to modify your pull settings, as 
such a process certainly can be carried out.  In the absence of actually seeing 
what your settings are, that's the best I can offer.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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