What version of cpptraj is on your laptop and what version is on the cluster?
-Dan
On Sat, Dec 16, 2017 at 10:25 AM, Rana Rehan Khalid <rrkhalid.umich.edu> wrote:
> 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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--
-------------------------
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
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Received on Mon Dec 18 2017 - 11:00:05 PST
