Yup, I re-ran it with rms fit and now the results are more reasonable. Thanks.! =)
Regards
Yip Yew Mun
Chemistry and Biological Chemistry
School of Physical and Mathematical Sciences
Nanyang Technological University
On 15-Jun-2013, at 12:10 AM, Carlos Simmerling wrote:
> This was addressed recently on the list, check the archive. It depends on
> the mask and the fitting for each case (rmsd and rmsf). I suspect in your
> case they are not the same.
> On Jun 14, 2013 11:59 AM, "Yip Yew Mun" <yipy0005.gmail.com> wrote:
>
>> Hi,
>>
>> Recently, one of my lab mates ran an MD simulation and she generated both
>> RMSD and RMSF graphs (nobox). We then observed that while the RMSD value is
>> ~ 3 Angstroms, the RMSF reached as high as 10 Angstroms and as low as 5
>> Angstroms. Therefore, I'm wondering if it's possible to have RMSF values
>> larger than RMSD values, because logically if a large RMSF is observed, it
>> should be captured in RMSD since it's calculated over time. What do you
>> guys think?
>>
>> Regards
>> Yip Yew Mun
>> Chemistry and Biological Chemistry
>> School of Physical and Mathematical Sciences
>> Nanyang Technological University
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Received on Sat Jun 15 2013 - 06:30:02 PDT
