-
Notifications
You must be signed in to change notification settings - Fork 13
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
About the rotation of the methyl group #18
Comments
That does not look good. I'll have a look when I can.
I suggest adding:
Then the dihedral scan is done by GROMACS (much faster), and you will also get all the fragment topologies and optimized geometries. Then you can investigate your issue further to narrow down the cause. |
@selimsami Thanks for the advice, I wonder how do I use Gromacs to do the scan?
Then I run
Please find the files attached |
It seems you're simply missing the QM dihedral scan output? Gaussian is still used for the QM part. GROMACS will be used for the MD scan (assuming that you already have the QM data) |
@selimsami Well, it seems that using the gmx MD engine solves the problem |
Great. Then probably it is an issue with the MD geometry optimization. GROMACS optimizer seems to be better than the scipy one. I normally use GROMACS for the MD engine, I suggest you to do the same. |
I'm testing a sample molecule.
It seems that the potential of rotating the methyl group (stick) is giving a large energy deviation.
I first suspect that it is a charge issue, but it seems that the charge of the three hydrogens in the methyl group are 0.135416, 0.109544, 0.107681 so this probably won't give such a large energy fluctuation.
I wonder if you mind having a check? Thank you.
Is it possible to have the topology file for the fragment as well? So I could see what is going wrong here.
Please find the example attached.
Archive.zip
The dihedral is scan_data_CC_H12C9O1_c08240069d2302aefe34ef147e3de1a7
The text was updated successfully, but these errors were encountered: