# Positive potential and Pressure scaling more than 1%

**URL:** <https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347>\
**Category:** User discussions\
**Created:** [February 16, 2024, 1:32pm UTC](https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347 "2024-02-16T13:32:59Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\
**Post date:** [February 16, 2024, 1:32pm UTC](https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347/1 "2024-02-16T13:32:59Z")

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Dear all

I am currently simulating some protein-protein complexes. I am getting a positive potential for a few complexes. Please let me know how to make it negative or if I can proceed with equilibration. I am simulating in water with 0.15M NaCl at 310K. I have the number of steps as 6000 instead of 50000 as the 50000 is giving other errors.

 ![Screenshot from 2024-02-16 15-21-12](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/4/4aed61f784544d40153cbf910d51dc9bd2f6fc56.png)  
 ![Screenshot from 2024-02-16 15-22-00](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/8/89f5462d7ed60ad016b844de7f2cdcd98cff67df.png)

The minimimsation anyways stops as soon as F\<1000. How to extent minimisation even after F\<1000?

For other complexes, I am getting the following error after npt:

Pressure scaling more than 1%. This may mean your system is not yet equilibrated. Use of Parrinello-Rahman pressure coupling during equilibration can lead to simulation instability, and is discouraged.  
I saw this post ([Pressure scaling more than 1%](https://gromacs.bioexcel.eu/t/pressure-scaling-more-than-1/2072)) about using Berendsen. So how is this carried out. First change to berendsen then what output file to use as the input for Parrinello-Rahman?

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [February 16, 2024, 2:33pm UTC](https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347/2 "2024-02-16T14:33:34Z")

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Do you have the force tolerance set to 1000? If so, lower it.

Force pressure coupling we always advise to use the c-rescale barostat. That message about using Berendsen is outdated and we have recently changed it to suggeset c-rescale.

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**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\
**Post date:** [February 17, 2024, 9:23pm UTC](https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347/3 "2024-02-17T21:23:29Z")

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Thank you for your response. I will lower the force.

Regarding the pressure scaling, should I always use c-rescale or try Parrinello Rahman first then if it does not work, change to c-rescale?

Thank you.

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**Author:** ![hess](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/hess/32/416_2.png) [@hess](https://gromacs.bioexcel.eu/u/hess)\
**Post date:** [February 19, 2024, 9:22am UTC](https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347/4 "2024-02-19T09:22:16Z")

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We suggest to always use c-rescale. It produces the correct ensemble without the risk of resonance problem that Parrinello-Rahman has.

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**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\
**Post date:** [February 19, 2024, 10:40am UTC](https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347/5 "2024-02-19T10:40:55Z")

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Thank you. I will change to c-rescale.

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**Author:** ![AF1](https://avatars.discourse-cdn.com/v4/letter/a/eada6e/32.png) [@AF1](https://gromacs.bioexcel.eu/u/AF1)\
**Post date:** [February 26, 2024, 9:40am UTC](https://gromacs.bioexcel.eu/t/positive-potential-and-pressure-scaling-more-than-1/8347/6 "2024-02-26T09:40:08Z")

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Hello

Last time you mentioned about lowering the force tolerance. I did it and I am successfully getting a potential negative for some structure. However, there are some with potential still showing positive even after I decreased emtol to 10 kJ/mol/nm. Could you please let me know if I can decrease emtol to a negative value? Thank you.