<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt"><div><br></div><div style="font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font face="Tahoma" size="2"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Mark Abraham <Mark.Abraham@anu.edu.au><br><b><span style="font-weight: bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Friday, January 28, 2011 17:51:41<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] invacuo simulation<br></font><br>
On 28/01/2011 8:45 PM, Kwee Hong wrote:
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<div style="color: rgb(0, 0, 0); font-family: arial,helvetica,sans-serif; font-size: 10pt;">Hi</div>
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In John's "GROMACS tutorial for solvation study of spider
toxin peptide",I keep on getting an error message at the
production stage: <br>
<br>
<br>
Step 12111 Warning: Pressure scaling more than 1%.<br>
<br>
Step 12121 Warning: Pressure scaling more than 1%.<br>
<br>
Step 12131 Warning: Pressure scaling more than 1%.<br>
<br>
-------------------------------------------------------<br>
Program mdrun, VERSION 4.5.1<br>
Source code file: ns.c, line: 2544<br>
<br>
Fatal error:<br>
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.<br>
For more information and tips for troubleshooting, please
check the GROMACS<br>
<span>website at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/Documentation/Errors">http://www.gromacs.org/Documentation/Errors</a></span><br>
<br>
I've tried a few approaches after reading the mailing list yet
I'm still getting the same error message.<br>
<br>
The command lined I used in this simulation is as follow:<br>
pdb2gmx -ignh -ff gtomos43a1 -f 1OMB.pdb -o fws.pdb -p fws.top
-water spce<br>
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Typo there.<br><br><span style="color: rgb(0, 96, 191);">Sorry for the typo</span><br>
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<div>editconf -bt cubic -f fws.pdb -o fws.pdb -d 1.0<br>
grompp -f em.mdp -c fws.pdb -p fws.top -o em.tpr -maxwarn 5<br>
mdrun -v -deffnm em<br>
grompp -f md.mdp -c em.gro -p fws.top -o md.tpr -maxwarn 3<br>
mdrun -v -deffnm md<br>
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Look at those warnings. Unless you know what they are and why
ignoring them is OK, don't use -maxwarn.<br>
<br><span style="color: rgb(0, 0, 191);">There is actually no warning but note: </span><br style="color: rgb(0, 0, 191);"><br style="color: rgb(0, 0, 191);"><span style="color: rgb(0, 0, 191);">The optimal PME mesh load for parallel simulations is below 0.5 and for highly parallel simulations between 0.25 and 0.33, for higher performance, increase the cut-off and the PME grid spacing</span><br style="color: rgb(0, 0, 191);"><br style="color: rgb(0, 0, 191);"><span style="color: rgb(0, 0, 191);">I think this is not significant since I'm running the simulation on single workstation.</span><br><br>
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After getting the error above round step 2300, I increased the
tau_p from 0.5 to 1.0.<br>
<br>
Yet I got the same error message at step 5400 though the
warning on pressure scaling more than 1% was gone. <br>
Therefore, I inceased the -d option in editconf to 1.5.<br>
<br>
But once again, I got the same error message at step 7300 (no
warning on pressure scaling). <br>
So once again, I increased the -d option in editconf to 2.5.<br>
<br>
And I still got the same error message at step 11300.<br>
<br>
I'm now real lost in solving this.. I hereby attach my
full.mdp file, hopefully to get some insight here.<br>
Any suggestions are appreciated.<br>
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.mdp file looks OK.<br>
<br>
Mark<br>
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Thanks.<br>
<br>
Regards,<br>
Joyce<br>
<br>
<br>
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