Thanks Dr. Roe
I am still confused, I used run data, runannalysis hist as u mentioned, but still cannot get the right representation for density map of RMSD Rg as in attached image
Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.
Emails:
mohamed_marzouk.sci.asu.edu.eg
marzouk.aa.m.titech.ac.jp
marzouk_biophysics.yahoo.com
mohamedmarzoukphysics.gmail.com
Mob. and WhatsApp.:
+81 070-4070-9549
+2 01061417414
> On Oct 15, 2 Reiwa, at 3:48 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> Hi,
>
> There was no attached photo, but what I assume you want to do is
> create a 2D histogram using your RMSD and radius of gyration data,
> right? You can do this by reading your RMSD/RoG data back into cpptraj
> and using the 'hist' analysis command, e.g.:
>
> readdata rmsd.dat name RMSD
> readdata rog.dat name ROG
> runanalysis hist RMSD:2 ROG:2 bins 100 out rmsd-rog-hist.gnu
>
> This is assuming that rmsd.dat and rog.dat are data files with the
> RMSD/RoG values in the 2nd column (hence the RMSD:2, ROG:2). See the
> manual for full details and keywords for the 'hist' command (it has a
> lot!). Hope this helps,
>
> -Dan
>
> On Mon, Oct 12, 2020 at 2:01 PM mohamed marzouk
> <mohamedmarzoukphysics.gmail.com> wrote:
>>
>> Hello,
>> After I finished simulation I want to do density map between RMSD and Rg such as attached photo.
>> I used cpptraj to get RMSD vs frames and Rg vs frames. How can I get this map
>>
>>
>>
>>
>>
>> Best regards,
>> Mohamed Marzouk Sobeh
>> Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
>> T.A Physics department,Ain Shams University, Cairo, Egypt.
>> Emails:
>> mohamed_marzouk.sci.asu.edu.eg
>> marzouk.aa.m.titech.ac.jp
>> marzouk_biophysics.yahoo.com
>> mohamedmarzoukphysics.gmail.com
>>
>> Mob. and WhatsApp.:
>> +81 070-4070-9549
>> +2 01061417414
>>
>>
>>
>>
>>
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>> AMBER mailing list
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Received on Tue Oct 20 2020 - 11:30:02 PDT
