[gmx-users] Distances calculation in umbrella sampling

Fri Dec 1 12:39:05 CET 2017

Hi
Replace the name of groups in original script by the names in between which
you want to measure the distance

Good luck!

On Dec 1, 2017 5:50 PM, "Kingsley Theras Primus Dass ." <
105726107 at gms.tcu.edu.tw> wrote:

> dear users,
>  I am encountering a problem with script, the summary.dat file does
> not generate
> any value. But if I run the distance command one at the time , it is
> generating the value, I could not figure out where I am goingperlgmx wrong.
> can anyone tell where lies the mistake?mistake?
>
>
> Thank you
>
> *below the command line for one distance *
> Command line:
>   gmx_mpi distance -s sgdp_pull_t.tpr -f conf1.pdb -n index.ndx -oall
> dist1.xvgtpr -f conf1.pdb -n index.ndx -oall dist1.xvg -n index. -
> dist1.xvg
> pdbndxoall
>
> Available static index groups:
>  Group 0 "System" (89993 atoms)
>  Group 1 "Protein" (6541 atoms)
>  Group 2 "Protein-H" (5087 atoms)
>  Group 3 "C-alpha" (644 atoms)
>  Group 4 "Backbone" (1932 atoms)
>  Group 5 "MainChain" (2578 atoms)
>  Group 6 "MainChain + Cb" (3192 atoms)
>  Group 7 "MainChain + H" (3209 atoms)
>  Group 8 "SideChain" (3332 atoms)
>  Group 9 "SideChain-H" (2509 atoms)
>  Group 10 "Prot-Masses" (6541 atoms)
>  Group 11 "non-Protein" (83452 atoms)
>  Group 12 "Other" (12949 atoms)
>  Group 13 "_ *" (19 atoms)
>  Group 14 "GDP" (34 atoms)
>  Group 15 "POPC" (12896 atoms)
>  Group 16 "NA" (107 atoms)
>  Group 17 "CL" (106 atoms)
>  Group 18 "Water" (70290 atoms)
>  Group 19 "SOL" (70290 atoms)
>  Group 20 "non-Water" (19703 atoms)
>  Group 21 "Ion" (213 atoms)
>  Group 22 "_ *" (19 atoms)
>  Group 23 "GDP" (34 atoms)
>  Group 24 "POPC" (12896 atoms)
>  Group 25 "NA" (107 atoms)
>  Group 26 "CL" (106 atoms)
>  Group 27 "Water_and_ions" (70503 atoms)
>  Group 28 "Protein_chain_A" (3536 atoms)
> Specify any number of selections for option 'select'
> (Position pairs to calculate distances for):
> (one per line, <enter> for status / groups, 'help' for help, Ctrl-D to end)
>
> > Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
> Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision)
> Reading frame 0 time 10.000 '', 89993 atoms
> Last frame 0 time 10.000
> Analyzed 1 frames, last time 0.000
> GDP:
>   Number of samples: 17
>   Average distance: 0.16202 nm
>   Standard deviation: 0.05626 nm
> Protein_chain_A:
>   Number of samples: 1768
>   Average distance: 0.19869 nm
>   Standard deviation: 0.12505 nm
>
>
>
> the error message that I get when I run perl script perl script
>
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> readline () on closed filehandle IN at distances.pl line 16.
> Use of uninitialized value $ distance in concatenation (.) Or string at
> distances.pl line 30.
> Cleaning up ...
>
>
>
> 2017-11-30 23:10 GMT+08:00 Amir Zeb <zebamir85 at gmail.com>:
>
> > Solved it,
> >
> > Thanks every one!
> >
> > Amir
> >
> > On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 11/30/17 4:04 AM, Rose wrote:
> > >
> > >> Till nowi think the only solution is to use gmx distance for each
> > >> conf.gro files.then use perl script.
> > >> don't forget to delete gmx distance line from script.
> > >>
> > >
> > > Or run one instance of gmx distance manually to understand how to
> > properly
> > > use it, diagnose any problems in your selection, etc. and fix the
> script.
> > > There's no reason to reinvent the wheel, just modify the script
> properly
> > to
> > > suit your needs.
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > Justin A. Lemkul, Ph.D.
> > > Assistant Professor
> > > Virginia Tech Department of Biochemistry
> > >
> > > 303 Engel Hall
> > > 340 West Campus Dr.
> > > Blacksburg, VA 24061
> > >
> > > jalemkul at vt.edu | (540) 231-3129
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==================================================
> > >
> > >
> > > --
> > > Gromacs Users mailing list
> > >
> > > * Please search the archive at http://www.gromacs.org/Support
> > > /Mailing_Lists/GMX-Users_List before posting!
> > >
> > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > >
> > > * For (un)subscribe requests visit
> > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > > send a mail to gmx-users-request at gromacs.org.
> > >
> > --
> > Gromacs Users mailing list
> >
> > * Please search the archive at http://www.gromacs.org/
> > Support/Mailing_Lists/GMX-Users_List before posting!
> >
> > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> >
> > * For (un)subscribe requests visit
> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-request at gromacs.org.
> >
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/
> Support/Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>