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Urgent Problem with Martini Tutorial.!
- yipy0005
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9 years 9 months ago #3920
by yipy0005
Urgent Problem with Martini Tutorial.! was created by yipy0005
While attempting the tutorial, at the equilibration step I received this error message:
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.
What can I do to resolve this?
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.
What can I do to resolve this?
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- Clement
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9 years 9 months ago #3921
by Clement
Replied by Clement on topic Urgent Problem with Martini Tutorial.!
More information? What tutorial?
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- yipy0005
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9 years 9 months ago #3922
by yipy0005
Replied by yipy0005 on topic Urgent Problem with Martini Tutorial.!
Hi, really really appreciate your prompt reply. The tutorial I'm talking about is the "Soluble protein: the Martini description" at
md.chem.rug.nl/cgmartini/index.php/proteins#martini
when I tried to execute this command:
grompp -f equilibration.mdp -c minimization.gro -p system.top -o equilibration.tpr
=D
grompp -f equilibration.mdp -c minimization.gro -p system.top -o equilibration.tpr
=D
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9 years 9 months ago #3925
by Clement
Replied by Clement on topic Urgent Problem with Martini Tutorial.!
You sure it's this command? Or during a mdrun... If it is, check your box size (last line), it might be wrong in your minimization.gro.
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- yipy0005
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9 years 9 months ago #3929
by yipy0005
Replied by yipy0005 on topic Urgent Problem with Martini Tutorial.!
I found the error to be the box size given by the tutorial to be too small. I changed it from 1.5 to 5 and it worked well again. =)
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9 years 9 months ago #3931
by Clement
Replied by Clement on topic Urgent Problem with Martini Tutorial.!
Check the density of your system... Can't have vacuum in there.
For what system did you make that change?
For what system did you make that change?
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- yipy0005
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9 years 9 months ago #3933
by yipy0005
Replied by yipy0005 on topic Urgent Problem with Martini Tutorial.!
It was for the ubiquitin protein from the tutorial.
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9 years 9 months ago #3936
by Clement
Replied by Clement on topic Urgent Problem with Martini Tutorial.!
What happen to the box dimensions during the following simulation? You can extract it from your .edr file with g_energy. Check the extend of the decrease... And check for vacuum bubble by visualize your system with VMD or whatnot.
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- yipy0005
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9 years 9 months ago #3937
by yipy0005
Replied by yipy0005 on topic Urgent Problem with Martini Tutorial.!
Okie, will do that and post my findings so that others can learn from it too. =)
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