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Visualization in tutorial(Lipid)
- tkim
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7 years 5 months ago #6297
by tkim
Visualization in tutorial(Lipid) was created by tkim
Hello,
I am new to CG and writing to ask a question about visualization with VMD.
I followed tutorial: Lipid and I could see how to form lipid bilayers.
But, several atoms are out of periodic boundary. So, this looks strange.
What I did is that I used trjconv and moved structures into periodic boundary to make new *.gro file.
The problem is when I typed "cg_bond -gmx
-tpr XXX.tpr" in TkConsole, the number of molecules are different between new *.gro file and *.tpr file.
This is what I have done, and would you share your experience for this?
Thank you
I am new to CG and writing to ask a question about visualization with VMD.
I followed tutorial: Lipid and I could see how to form lipid bilayers.
But, several atoms are out of periodic boundary. So, this looks strange.
What I did is that I used trjconv and moved structures into periodic boundary to make new *.gro file.
The problem is when I typed "cg_bond -gmx
-tpr XXX.tpr" in TkConsole, the number of molecules are different between new *.gro file and *.tpr file.
This is what I have done, and would you share your experience for this?
Thank you
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- peterkroon
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7 years 5 months ago #6309
by peterkroon
Replied by peterkroon on topic Visualization in tutorial(Lipid)
If you only moved molecules, and you end up with a different number of molecules something went *very* wrong, so check your output.
Alternatively (say you want to remove waters), make new tpr.
Alternatively (say you want to remove waters), make new tpr.
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