[gmx-users] invacuo simulation

[Mark Abraham]

On 28/01/2011 8:45 PM, Kwee Hong wrote:
> Hi
>
> 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

Typo there.

> 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

Look at those warnings. Unless you know what they are and why ignoring 
them is OK, don't use -maxwarn.

>
> After getting the error above round step 2300, I increased the tau_p 
> from 0.5 to 1.0.
>
> 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.

.mdp file looks OK.

Mark

>
> Thanks.
>
> Regards,
> Joyce
>
>
>

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