[gmx-users] invacuo simulation

Kwee Hong jestan1985 at yahoo.com
Fri Jan 28 10:45:54 CET 2011

In John's "GROMACS tutorial for solvation study of spider toxin peptide",I keep 
on getting an error message at the production stage: 

Step 12111  Warning: Pressure scaling more than 1%.

Step 12121  Warning: Pressure scaling more than 1%.

Step 12131  Warning: Pressure scaling more than 1%.

Program mdrun, VERSION 4.5.1
Source code file: ns.c, line: 2544

Fatal error:
One of the box vectors has become shorter than twice the cut-off length or 
box_yy-|box_zy| or box_zz has become smaller than the cut-off.
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

I've tried a few approaches after reading the mailing list yet I'm still getting 
the same error message.

The command lined I used in this simulation is as follow:
pdb2gmx -ignh -ff gtomos43a1 -f 1OMB.pdb -o fws.pdb -p fws.top -water spce
editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0
grompp -f em.mdp -c fws.pdb -p fws.top -o em.tpr -maxwarn 5
mdrun -v -deffnm em
grompp -f md.mdp -c em.gro -p fws.top -o md.tpr -maxwarn 3
mdrun -v -deffnm md

After getting the error above round step 2300, I increased the tau_p from 0.5 to 

Yet I got the same error message at step  5400 though the warning on pressure 
scaling  more than 1% was gone. 

Therefore, I inceased the -d option in editconf to 1.5.

But once again, I got the same error message at step 7300 (no warning on 
pressure scaling). 

So once again, I increased the -d option in editconf to 2.5.

And I still got the same error message at step 11300.

I'm now real lost in solving this.. I hereby attach my full.mdp file, hopefully 
to get some insight here.
Any suggestions are appreciated.



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