[gmx-users] Rectangular vs triclinic boxes

[Ivano Eberini]

Dear Erik,
many thanks for your reply.


> Anyway - is there something special with the 4th simulation, and are you
> able to run
> any steps at all?

I prepared all the 4 simulations in the same manner, so I assume there 
is nothing  peculiar. I followed these steps: setting a rectangular box, 
water addiction, EM, restrained MD and then 3 ns not restrained MD. The 
one which crashed run for 1 ns (500,000 steps), while the others 
finished MD calculation, apparently without any problem.

>  From the above error my first guess would be that
> something happens
> to your system so you get a very high veolcity somewhere (e.g. close
> contact), and
> then everything crashes (since the NaNs are propagated to the box size).
> Have you
> tried a smaller timestep and/or more minimization?

I can try either with more minimization or with reduced timestep (from 
0.002 ps I used, to 0.001 ps) or both; which one of these do you think 
is the more likely to work?

May I ask you another question? I looked at the trajectory of a long 
time MD. After 1.5 ns the protein exited partially from the box. Have I 
got to run again MD with a larger/different box or can I use data 
already obtained? I read on Gromacs manual that MD is calculated in a 
system composed by periodic repeats of the unit box.

Thanks in advance.

Bye,
Ivano