[gmx-developers] How to make protein whole in do_force, Warning: 1-4 interaction between 567 and 575 at distance 5.695 which is larger than the 1-4 table size 1.000 nm

[Jason de Joannis]

I don't see why going out of the box should harm the simulation unless 
you have modified Gromacs in such a way that affects the periodic 
boundary conditions. More likely is that you prepared an unstable 
system that explodes (have you tried running it with unmodified 
Gromacs?). If this is a Gromacs usage question then it belongs on the 
gmx-users mailing list.

Quoting mchen2 at mailer.fsu.edu:

> you guys,
> My system always crashes with /*
> Warning: 1-4 interaction between 567 and 575 at distance 5.695 which 
> is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> Warning: 1-4 interaction between 567 and 575 at distance 6.236 which 
> is larger than the 1-4 table size 1.000 nm
> and LINCS errors ... */
> I'm pretty sure that it's caused by the broken topology of protein. 
> Because it happens when partial structure of protein(side chain) went 
> out the box(my water box is 6.5, 6.5, 6.5, and here 567 and 575 are 
> the "CD" and "HZ3" atoms of LYS, and the "NH3" is out of box).
> It say "The coordinates (x) are shifted (to get whole molecules) in 
> do_force" in "md.c" sourcecode, but I cannot find any shifts in 
> "do_force()" except the routines of put_charge_groups_in_box() and 
> mk_mshift(). Actually I did a little adaption based on the 
> sourcecode(ver3.3.1). I'm sure I alternate the code properly except: 
> I call "do_force()" for many times in one step md loop like that 
> "minimize.c" do;  After each "do_force()", "unshift_self()" was 
> called.
> It's really vexatious, help me!
> Can you guys check the "do_force()" section, tell me how to make the 
> molecule whole properly or it's my misunderstanding totaly.
> Thanks
> Mengen Chen
>



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