normal Unstable simulation after replicatio

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9 years 6 months ago #4075 by ozma
Dear all
I have a coarse grained simulation box containing membrane protein, lipid membrane and water molecules which runs well in GROMACS. But after replication with genbox for 16 (4,4,1) times, the system does not stay stable anymore.
Is there any suggestions?

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9 years 6 months ago #4076 by Clement
Replied by Clement on topic Unstable simulation after replicatio
Well, we would need more information here... What is happening? What is not stable? How does the simulation crash?

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9 years 5 months ago #4094 by ozma
Replied by ozma on topic Unstable simulation after replicatio
It give too many lincs warning.

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9 years 5 months ago #4096 by Clement
Replied by Clement on topic Unstable simulation after replicatio
What gives the LINCS warnings, where is it unstable?
How long did you simulate the first box?
What's the genconf command line you use to replicate the box?
Did you do another round of energy minimization/equilibration (lower time step) after replicating?

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9 years 5 months ago #4100 by ozma
Replied by ozma on topic Unstable simulation after replicatio
Dear Clement thanks, but I think the issue is solved now.
Actually the problem was that when I used genbox to replicate the system, I didn't write the molecules in top file according to their sequence in conf file.

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9 years 5 months ago #4101 by Clement
Replied by Clement on topic Unstable simulation after replicatio
That would make everything quite unstable indeed. Well, glad you found out!

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