Using ParmEd

The functionality of OpenMM will (eventually) include everything that one would need to run modern molecular simulation.
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Tej Tarun Sharma
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Joined: Fri Oct 11, 2024 7:01 am

Using ParmEd

Post by Tej Tarun Sharma » Fri Oct 11, 2024 7:18 am

Hi, I created the 'ParmEd structure' instance from 'openMM system' and after that, I saved the amber parameter file and coordinate file from the ParmEd structure because I want to use Amber.
But when I am calculating the system's potential energy in Amber, I am getting it different from what I got using openMM. What could be the possible reason for this?
Thanks.
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Peter Eastman
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Joined: Thu Aug 09, 2007 1:25 pm

Re: Using ParmEd

Post by Peter Eastman » Mon Oct 14, 2024 9:08 am

Is this a question about OpenMM or ParmEd? If the latter, I can't help with that.

If it's a question about OpenMM, can you show your code? If possible, give a complete test case that can be used to reproduce the problem, including all input files.
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Tej Tarun Sharma
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Joined: Fri Oct 11, 2024 7:01 am

Re: Using ParmEd

Post by Tej Tarun Sharma » Thu Oct 17, 2024 10:15 pm

Sorry, I think it is a conversion issue because I have noticed some unusual zeroes in the dihedral force constants in the amber .prmtop file.
Thank you,
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