Dear Justin and Peter,
Thank you so much! I did not realise the meaning of two prompts until
now. I was always using the same number for the two prompts.
Thank you for the MDAnalysis!
https://www.mdanalysis.org/pages/learning_MDAnalysis/
Yours sincerely
Cheng
--
On 24-11-17 13:48, Justin Lemkul wrote:
>
>
> On 11/24/17 5:25 AM, ZHANG Cheng wrote:
>> Dear Justin,
>> Thank you for confirming this. May I ask,
>>
>>
>> 1) How to "fit to the whole protein (or backbone, CA, etc) and
>> subsequently calculate the RMSD of given residue(s)"?
>>
>>
>> My current
On 11/24/17 5:25 AM, ZHANG Cheng wrote:
Dear Justin,
Thank you for confirming this. May I ask,
1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently
calculate the RMSD of given residue(s)"?
My current command is (by selecting the residue in the "index.ndx" file):
gmx
Dear Justin,
Thank you for confirming this. May I ask,
1) How to "fit to the whole protein (or backbone, CA, etc) and subsequently
calculate the RMSD of given residue(s)"?
My current command is (by selecting the residue in the "index.ndx" file):
gmx rms -s md_0_1.tpr -f md_0_1_noPBC.xtc -n
On 11/23/17 11:20 AM, ZHANG Cheng wrote:
Dear Gromacs,
When I calculate the RMSD for the whole protein, I got values mostly from
0.2-0.5 nm. However, when I only calculate for a particular residue (using an
index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the
loop.
Dear Gromacs,
When I calculate the RMSD for the whole protein, I got values mostly from
0.2-0.5 nm. However, when I only calculate for a particular residue (using an
index file), the scale is mostly only 0.01-0.02 nm, even for a residue on the
loop.
My understanding is: when doing the RMSD,
