[gmx-users] Regarding wired RDF of TMAO and Aminoacid

Christopher Neale chris.neale at alum.utoronto.ca
Thu Oct 5 07:47:03 CEST 2017

Please show us the plots (upload to a file hosting site and paste the link in your post) or precisely define your results; also explain precisely why the results are unexpected. Also show us your exact commands. Without this we can not help.

From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Dilip H N <cy16f01.dilip at nitk.edu.in>
Sent: 04 October 2017 23:48:08
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Regarding wired RDF of TMAO and Aminoacid

I have run an NPT MD simulation of an amino acid with TMAO (as a cosolvent)
and water for different concentration (by varying composition of cosolvent:
water). I have used Charmm36 FF for TMAO.
Now if i am plotting the RDF for Amino acid v/s Water in the presence of
different concentrations TMAO, I am getting wired RDF's for each
composition of TMAO present, the peaks are absurd.....
Why is this happening..?? i have looked into the final structure of my
simulation in VMD which is correct....
I am confused...
Any Suggestions are appreciated...

With Best Regards,

Ph.D Student

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