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> wrote:
> **Warning** The sender address ("Godbole, Shivani via AMBER" ) can not be
> verified, sender email address could be spoofed. Please take care to
> proceed.
> 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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--
*Dr. Thomas Steinbrecher*
Principal Scientist CADD
Roche Pharma Research and Early Development
Roche Innovation Center Basel
F. Hoffmann-La Roche Ltd
Bldg. 092/3.92
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4070 Basel
Switzerland
Phone +41 61 682 1319
mailto: thomas.steinbrecher.roche.com
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Received on Wed Feb 28 2024 - 09:30:02 PST
