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  5. Pressure scaling warning

normal Pressure scaling warning

  • kmcallenberg
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13 years 6 months ago #425 by kmcallenberg
Pressure scaling warning was created by kmcallenberg
Hi, I have run 3 test simulations with simple proteins in water and I am encountering pressure scaling errors with all of them, and the box size is changing constantly. This occurs even when I am following the instructions for the Protein Tutorial here on the Martini website. The warning does not go away in long simulations.

Here is an example of the warning:

Step 4999991 Warning: pressure scaling more than 1%, mu: 0.989586 0.989586 0.984892


Here are the gromacs steps I performed after coarse-graining the protein:
264  genbox -cp rop18_cg.pdb -o rop18_cg_box.gro -box 8 8 8
  266  grompp -f em.mdp -c rop18_cg_box.gro -p rop18_cg.top -maxwarn 10
  267  mdrun -v -c rop18_minimized.gro 
  269  genbox -cp rop18_minimized.gro -cs water-1bar-303K.gro -o rop18_w.gro -box 8 8 8 -vdwd 0.235
  270  nano rop18_cg.top
  271  grompp -f em.mdp -c rop18_w.gro -p rop18_cg.top -maxwarn 10
  272  mdrun -v -c rop18_w_minimized.gro
  273  grompp -f em.mdp -c rop18_w_minimized.gro -p rop18_cg.top -maxwarn 10
  274  genion -o rop18_w_ion_minimized.gro -nname CL- -nn 7
  275  nano md.mdp
  277  nano rop18_cg.top
  278  grompp -f md.mdp -c rop18_w_ion_minimized.gro -p rop18_cg.top -maxwarn 10
  279  mdrun -v -c rop18_w_ion_md.gro

Does anyone have any idea what this could be due to?

Thanks!

Keith Callenberg
University of Pittsburgh

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  • kmcallenberg
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13 years 6 months ago #427 by kmcallenberg
Replied by kmcallenberg on topic Pressure scaling warning
I think some of these issues may be fixed with position restraint MD, but so far either the system crashes or I receive errors when I try to impose restraints.

It would be helpful if someone could post command-by-command workflows for how they performed successful simulations with the Martini forcefield. This was done for the Bilayer self-assembly tutorial but not for the protein tutorial or anything more sophisticated.

Unlike system setup in VMD which is GUI-based, all that is necessary is posting the results from the Unix history command. Does anyone know of any such Martini tutorials? I will put a bit of time into posting my successful results on my blog if not.

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  • andrzej
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13 years 6 months ago #429 by andrzej
Replied by andrzej on topic Pressure scaling warning
The system that You simulate is not exactly the one from tutorial, wright ?

Have You checked the FAQ section ?

md.chem.rug.nl/cgmartini/index.php/user-platform/faq#crashing

Check the energy file for what causes the problem, the box fluctuations and pressure deviations are results caused by other problems.

Andrzej

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