CHARMM Development Project
Posted By: cg_nanome FEP output file? - 12/07/21 04:52 PM
We're working on a GROMACS integration and would like to be able to support FEP files types. Does anyone have an FEP output file they would be willing to share for testing purposes only? (It will not be published or used in any other way). Thanks.
Posted By: rmv Re: FEP output file? - 12/07/21 05:36 PM
CHARMM has a variety of methods for FEP so you may need to be more specific, although I'm not sure how much any of them would help with a GROMACS issue.
Posted By: lennart Re: FEP output file? - 12/07/21 09:11 PM
You may want to address this question to GROMACS support, if it exists. This site is for CHARMM questions (perhaps the URL www.CHARMM.org/... is misleading?)
The scientific approach here is of course to produce the desired file yourself.
Posted By: cg_nanome Re: FEP output file? - 12/13/21 02:21 PM
Thx for replies...I probably shouldn't have mentioned GROMACS at all- we're just thinking of using the CHARMM-GUI to set up calculations for it. Really what we want to do right now is be able to have our software support FEP file types- specifically an output file. For this purpose, it would be quicker for us if someone already has one they don't mind sharing until we have the integration set up and can generate them ourselves.
Posted By: rmv Re: FEP output file? - 12/13/21 02:58 PM
There are at least 3 different implementations for free energy perturbation in CHARMM, with different output. To the best of my knowledge, no one with expertise in any of them is a regular contributor to these forums.
Posted By: lennart Re: FEP output file? - 12/13/21 04:49 PM
It seems to me that you should run the FEP calculations yourself - how could anybody trust your software's support of FEP file types, if you manifestly have no idea of what is going on?
Posted By: cg_nanome Re: FEP output file? - 01/27/22 05:39 AM
@lennart We have experience running many FEP calculations using proprietary software for which it is not possible to read the file outputs unless you are a subscriber to that particular tool. Our company aims to democratize access to FEP file visualization so we are looking at the open source methods. We already support many different file types for visualization in virtual reality.
Posted By: cg_nanome Re: FEP output file? - 01/27/22 05:43 AM
@rmv thank you for your straightforward and honest reply. Looks like I need to look elsewhere for FEP in CHARMM.
Posted By: lennart Re: FEP output file? - 01/27/22 11:46 AM
CHARMM FEP methods are open source
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