[gmx-users] Translating my system using editconf causes my run to crash!

[S. Alireza Bagherzadeh]

Hi everyone,

I am using "editconf" to translate my system along the z-axis.

However, by trial and error I realized that only at some values of the
z-component of the translation vector I am able to run my system, otherwise
my run produces a number of stepN.pdb files with the following output:
---------
Getting Loaded...
Reading file topol.tpr, VERSION 4.5.5 (single precision)
Loaded with Money

Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.1#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.1#
Wrote pdb files with previous and current coordinates
starting mdrun 'Methane hydrate between 2 silica surfaces in contact with
water and gas'
500000 steps,    500.0 ps.
Shake did not converge in 1000 steps

Back Off! I just backed up step0b.pdb to ./#step0b.pdb.2#

Back Off! I just backed up step0c.pdb to ./#step0c.pdb.2#
Wrote pdb files with previous and current coordinates
step 0Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
....
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
step 100, will finish Thu Feb  7 12:49:37 2013Shake did not converge in
1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
...

[So, I do Ctrl+C to break the run]

Received the INT signal, stopping at the next NS step

Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
step 300, will finish Thu Feb  7 13:12:45 2013Shake did not converge in
1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
Shake did not converge in 1000 steps
Wrote pdb files with previous and current coordinates
step 310, will finish Thu Feb  7 13:16:46 2013
               NODE (s)   Real (s)      (%)
       Time:    104.820    106.221     98.7
                       1:44
               (Mnbf/s)   (GFlops)   (ns/day)  (hour/ns)
Performance:     21.511      1.739      0.256     93.623
--------

I am using this command:
editconf -f conf.gro -translate 0 0 Vz -o conf-translated.gro

if Vz = 5, 10 or 35 -> no error!
if Vz = 15, 20, 25 or 35 -> error!

I have 58883 atoms in my conf.gro file with the following simulation box:
3.60900   6.60800  28.64862


This looks so strange to me! Why just translating over the z-axis causes
any problem in my system??!!!

Have you ever had this experience with gormacs? Would you have an insight
on why this is happening?


Best regards,


-- 
S. Alireza Bagherzadeh
PhD Candidate
Dept. of Chem. & Bio. Eng.
University of BC
2360 East Mall
Vancouver BC V6T1Z3