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
--
========================================
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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