I am trying to induce conformational changes with lower pH for which I need a higher RMSD value to justify that my system is active at a lower pH than the physiological pH. Does 3A justify that conformational change?
I am new at MD simulations and am still learning.
Thank you,
Shivani
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Hi Shivani,
why do you consider this a problem? In general, a stable MD simulation of a typical protein will result in RMSD values rising to around 2A over several 100ns. Are there conformational changes you expect and do not see in your runs? Otherwise, your result may just be in the expected range of outcomes.
Kind Regards,
Thomas
On Wed, Feb 28, 2024 at 6:06 PM Godbole, Shivani via AMBER <amber.ambermd.org<mailto:amber.ambermd.org>> wrote:
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Hello,
This is Shivani Godbole. I am running Constant pH Md simulations for my proteins. I have noticed the RMSD values after running the cpptraj command are quite low (around 3 A). What can be done about this?
Thank you,
Shivani Sujay Godbole, B. Pharm
Biomedical Sciences, Ph.D. Student
Penn State College of Medicine
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Received on Wed Feb 28 2024 - 09:30:03 PST
