Hi,
On Fri, Apr 16, 2021 at 11:23 AM waleed zalloum
<waleed_zalloum.yahoo.com> wrote:
>
> readdata evecs-ca.dat name pc1
> readdata evecs-ca.dat name pc2
Did this give an error? You didn't specify. Assuming there is indeed
"modes" data in evecs-ca.dat you should see a message like:
Reading 'evecs-ca.dat' as Evecs file with name 'pc1'
Also, you don't need to specify the same file twice. By default
cpptraj will read all modes from the file.
> runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 1 out rmsip
You're doing the RMSIP of eigenvector 1 to 1 which is not very useful.
Try 'beg 1 end 2' instead.
>
>
> Also, I projected the trajectory coordinates along pcs and got a file for this process (pca12-ca). I tried to read it instead of evecs-ca.dat in the above comman but it gave me the following error:
No, this won't work. Projections are not the same as "modes" (i.e.
eigenvectors). You can use eigenvectors to get projections, but you
can't feed the projection values back in place of modes.
Hope this helps,
-Dan
>
> INPUT: Reading Input from file pcin-emsip
> [readdata pca12-ca name pc1 ]
> Reading 'pca12-ca' as Standard Data File with name 'pc1'
> DataFile pca12-ca has 4 columns, 62501 lines.
> DataFile contains labels:
> 1: Frame
> 2: Mode1
> 3: Mode2
> 4: Mode3
> Index column is 1
> [readdata pca12-ca name pc2]
> Reading 'pca12-ca' as Standard Data File with name 'pc2'
> DataFile pca12-ca has 4 columns, 62501 lines.
> DataFile contains labels:
> 1: Frame
> 2: Mode1
> 3: Mode2
> 4: Mode3
> Index column is 1
> [runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 1 out rmsip]
> Error: 'pc1' not found: Modes should be read in prior to this command with 'readdata'
>
> TIME: Total analysis execution time: 0.0000 seconds.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.0960 seconds.
>
> Also, I tried to read a file containing the first eigenvector and the other has 50 eignevector but it gave me a result of 1 as below.
>
> readdata evecs-firstvector-ca.dat name pc1
> readdata evecs-allvectors-ca.dat name pc2
> runanalysis modes rmsip name pc1 name2 pc2 beg 1 end 1 out rmsip
>
> I am not fully aware of what I have to do to calculate rmsip for each mode and then plot rmsip vs each mode.
>
> Thank you, indeed
>
> Waleed
>
> On Friday, 16 April 2021, 16:50:18 EEST, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
>
> Hi,
>
> On Fri, Apr 16, 2021 at 12:01 AM waleed zalloum
> <waleed_zalloum.yahoo.com> wrote:
> > I tried to used modes of cpptraj, but with no succes.
>
>
> Can you be more specific? What was the exact input you gave cpptraj?
> Did you try using 'mode rmsip'? Did you get an error message?
>
> -Dan
>
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Received on Fri Apr 16 2021 - 12:30:03 PDT
