Re: [AMBER] PCA.CPPTRAJ

From: Rana Rehan Khalid <rrkhalid.umich.edu>
Date: Sat, 16 Dec 2017 20:25:38 +0500

when I did the cpptraj pca analysis on my laptop and run the command one by
one it works but when i submit my job with the above mentioned script on
cluster it show these warnings and job again stop. Thanks

 [diagmatrix oxxx-covar out oxxx-evecs.dat \ ]
Warning: # of eigenvectors specified is < 1 (0) and 'thermo' not specified.
Warning: Specify # eigenvectors with 'vecs <#>'. Setting to 1.
        Changed DataFile 'oxxx-evecs.dat' type to Evecs file for set
Modes_00004
    DIAGMATRIX: Diagonalizing matrix oxxx-covar and writing modes to
oxxx-evecs.dat
        Calculating 1 eigenvectors
TIME: Total execution time: 230.3207 seconds.

On Sat, Dec 16, 2017 at 6:38 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
wrote:

> Hi sir Thank you. I understand now the point.I change the script as you
> guide and ran it works. kindly guide me if any thing wrong in it.
>
> Regards
>
> parm ox_solv.prmtop
> trajin oxy_1.mdcrd
> trajin oxy_2.mdcrd
> trajin oxy_3.mdcrd
> trajin oxy_4.mdcrd
> trajin oxy_5.mdcrd
> trajin oxy_6.mdcrd
> trajin oxy_7.mdcrd
> trajin oxy_8.mdcrd
> trajin oxy_10.mdcrd
> trajin oxy_11.mdcrd
> rms first :1-189&!.H=
> average crdset MyAverage
> run
> rms ref MyAverage :1-189&!.H=
> matrix covar name bay1-covar :1-189&!.H=
> diagmatrix bay1-covar out bbb-evecs.dat \
> vecs 3 name myEvecs \
> nmwiz nmwizvecs 3 nmwizfile bbb.nmd nmwizmask :1-189&!.H=
> run
> rms ref MyAverage :1-189&!.H=
> projection HNOX-O2 evecs bbb-evecs.dat myEvecs beg 1 end 3 :1-189&!.H=
> crdframes 1,70000
> run
> hist HNOX-O2:1 bins 100 out oxy-hist.agr norm name OXY-1
> hist HNOX-O2:2 bins 100 out oxy-hist.agr norm name OXY-2
> hist HNOX-O2:3 bins 100 out oxy-hist.agr norm name OXY-3
> run
> ##############
> clear all
> readdata bbb-evecs.dat name Evecs
> parm ox_solv.prmtop
> parmstrip !(:1-189&!.H=)
> parmwrite out oxx-modes.prmtop
> runanalysis modes name Evecs trajout oxx-mode1-10.nc \
> pcmin -100 pcmax 100 tmode 1 trajoutmask :1-189&!.H= trajoutfmt netcd
>
> On Sat, Dec 16, 2017 at 1:05 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
> wrote:
>
>> Hi
>> I am confused about the <option> I tried to compare it with other PCA
>> script and manual to get understanding but not get point. Is it mode data
>> set like .dat Kindly guide me. Thanks
>> diagmatrix bay1-covar name bay1-modes <options>
>> modes name bay1-modes <options>
>> projection MyProjection evecs bay1-modes <options>
>>
>> Regards
>>
>> On Thu, Dec 14, 2017 at 11:21 PM, Daniel Roe <daniel.r.roe.gmail.com>
>> wrote:
>>
>>> Hi,
>>>
>>> Try doing it without creating a COORDS data set - this stores all your
>>> coordinates in memory, which is convenient if you have the memory to
>>> spare, but in this case you do not. This means you need to modify your
>>> coordinates each time you process them (i.e. you need to rms-fit
>>> before you project etc). Something like:
>>>
>>> # First run to generate average structure
>>> trajin bay_1.mdcrd
>>> ...
>>> rms first <mask>
>>> average crdset MyAverage
>>> run
>>> # Second run to generate covariance matrix and modes. Also run modes
>>> analysis.
>>> rms ref MyAverage <mask>
>>> matrix covar name bay1-covar <mask>
>>> diagmatrix bay1-covar name bay1-modes <options>
>>> modes name bay1-modes <options>
>>> run
>>> # Example third run for projection
>>> rms ref MyAverage <mask>
>>> projection MyProjection evecs bay1-modes <options>
>>>
>>> Hope this helps,
>>>
>>> -Dan
>>>
>>>
>>>
>>>
>>> On Wed, Dec 13, 2017 at 4:58 PM, Rana Rehan Khalid <rrkhalid.umich.edu>
>>> wrote:
>>> > Dear Amber users
>>> >
>>> > I am trying to run the PCA script every time job stop due to this
>>> exceeded
>>> > limit of memory
>>> >
>>> > job 16802098 exceeded MEM usage hard limit (39282 > 2048)
>>> >
>>> > I use this script for running the job
>>> > #!/bin/bash
>>> > #PBS -l nodes=1:ppn=1
>>> > #PBS -l walltime=100:00:00
>>> > cd /nfs/amino-home/rrkhalid/bay60
>>> > /nfs/amino-library/local/Amber14/bin/cpptraj -p bay.prmtop -i
>>> pca.cpptraj
>>> >
>>> > and pca.cpptraj script is this each trajectory( 1-10 ) file run 750000
>>> > steps.
>>> > rajin bay_1.mdcrd
>>> > trajin bay_2.mdcrd
>>> > trajin bay_3.mdcrd
>>> > trajin bay_4.mdcrd
>>> > trajin bay_5.mdcrd
>>> > trajin bay_6.mdcrd
>>> > trajin bay_7.mdcrd
>>> > trajin bay_8.mdcrd
>>> > trajin bay_9.mdcrd
>>> > trajin bay_10.mdcrd
>>> > rms first :1-189&!.H=
>>> > average crdset average
>>> > createcrd avgtrajectories
>>> > run
>>> > crdaction avgtrajectories rms ref average :1-189&!.H=
>>> > crdaction avgtrajectories matrix covar name bay1-covar :1-189&!.H=
>>> > runanalysis diagmatrix bay1-covar out bay1-evecs.dat \
>>> > vecs 3 name myEvecs \
>>> > nmwiz nmwizvecs 3 nmwizfile bay.nmd nmwizmask :1-189&!.H=
>>> > ##########
>>> > clear all
>>> > readdata bay1-evecs.dat name Evecs
>>> > parm bay.prmtop
>>> > parmstrip !(:1-189&!.H=)
>>> > parmwrite out bay-modes.prmtop
>>> > runanalysis modes name Evecs trajout bay-mode1.nc \
>>> > pcmin -100 pcmax 100 tmode 1 trajoutmask :1-189&!.H= trajoutfmt netcd
>>> >
>>> > kindly guide Thanks
>>> > _______________________________________________
>>> > AMBER mailing list
>>> > AMBER.ambermd.org
>>> > http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
>>>
>>> --
>>> -------------------------
>>> Daniel R. Roe
>>> Laboratory of Computational Biology
>>> National Institutes of Health, NHLBI
>>> 5635 Fishers Ln, Rm T900
>>> Rockville MD, 20852
>>> https://www.lobos.nih.gov/lcb
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>
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Received on Sat Dec 16 2017 - 07:30:03 PST
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