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<DIV><FONT face=Arial>Mark advice helped me to solve my problem, </FONT></DIV>
<DIV><FONT face=Arial>now it works fine just the way I wanted. <BR>Manual says
“For constraints between </FONT></DIV>
<DIV><FONT face=Arial>molecules the pull code can be used…” and I </FONT></DIV>
<DIV><FONT face=Arial>wanted to know is there a simple way to do
this. </FONT></DIV>
<DIV><FONT face=Arial>Mark thank you for script, it works
fine.<BR>Michal<BR></DIV></FONT>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial></FONT> </DIV>
<DIV><FONT face=Arial>Uwe Richter wrote:<BR>><I> Hi Mark,<BR></I>><I>
<BR></I>><I> I assume Michal knows how to define distance restraints. That's
described<BR></I>><I> in the manual. <BR></I><BR>It would be good to be able
to assume that :-) Unfortunately my <BR>impression is that many people who post
haven't done enough work <BR>themselves on the problem... to the point that they
haven't read the <BR>manual (well enough). One could certainly interpret
Michal's question in <BR>the way you did, though!<BR><BR> > The problem is
you can't do this between different<BR>><I> 'molecules',<BR></I>><I> as
you know. I think 'molecule' might not be the best expression in this
<BR></I>><I> context.<BR></I><BR>Indeed, I carefully used the word
'topologies' - probably not perfect <BR>given the specific GROMACS usage, but
something like 'assemblies' or <BR>'systems' aren't quite right either...
'structures'?<BR><BR>><I> You can very well have many molecules in one
topology section, which has <BR></I>><I> the<BR></I>><I> advantage that it
is possible to define distance restraints between <BR></I>><I> them.
Of<BR></I>><I> course this setup also has its disadvantages. It really
depends on the <BR></I>><I> project.<BR></I><BR>That you have to merge the
topologies to be able to have the option of <BR>restraints is a good point - one
I hadn't encountered before. Thanks.<BR><BR>Mark<BR></DIV></FONT></BODY></HTML>