<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:arial,helvetica,sans-serif;font-size:10pt;color:#000000;"><div><div style="color: rgb(0, 0, 0); font-family: arial,helvetica,sans-serif; font-size: 10pt;">Hi</div><div style="color: rgb(0, 0, 0); font-family: arial,helvetica,sans-serif; font-size: 10pt;"><br></div>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 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>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><br>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><br>Thanks.<br><br>Regards,<br>Joyce<br><br><br></div>
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