[gmx-users] gromacs.org_gmx-users Digest, Vol 153, Issue 12

[Nivedita Rai]

Dear User,
                    while production run im getting two notes such as:

NOTE 1 [file topol.top]:
  The largest charge group contains 11 atoms.
  Since atoms only see each other when the centers of geometry of the charge
  groups they belong to are within the cut-off distance, too large charge
  groups can lead to serious cut-off artifacts.
  For efficiency and accuracy, charge group should consist of a few atoms.
  For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.

Number of degrees of freedom in T-Coupling group Protein_UNK is 8298.87
Number of degrees of freedom in T-Coupling group Water_and_ions is 180606.12
Largest charge group radii for Van der Waals: 0.267, 0.265 nm
Largest charge group radii for Coulomb:       0.267, 0.265 nm
Calculating fourier grid dimensions for X Y Z
Using a fourier grid of 84x84x84, spacing 0.118 0.118 0.118
Estimate for the relative computational load of the PME mesh part: 0.32

NOTE 2 [file md.mdp]:
  This run will generate roughly 5681 Mb of data

Is *note1* will create any trouble? if yes then how to rectify it?


On Thu, Jan 5, 2017 at 4:30 PM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

> Send gromacs.org_gmx-users mailing list submissions to
>         gromacs.org_gmx-users at maillist.sys.kth.se
>
> To subscribe or unsubscribe via the World Wide Web, visit
>         https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users
> or, via email, send a message with subject or body 'help' to
>         gromacs.org_gmx-users-request at maillist.sys.kth.se
>
> You can reach the person managing the list at
>         gromacs.org_gmx-users-owner at maillist.sys.kth.se
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of gromacs.org_gmx-users digest..."
>
>
> Today's Topics:
>
>    1. Regression test error in gromacs 5.1.4 installation
>       (Abhisheak Sharma)
>    2. Index file group selection and gmx covar error (Aditya Padhi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 5 Jan 2017 13:01:57 +0530
> From: Abhisheak Sharma <abhisheknano.cct at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Regression test error in gromacs 5.1.4
>         installation
> Message-ID:
>         <CADCycEwEq96D0ksMN1UiyO4v-B+UgmQx0mCNG7TTphPLF6KO0w at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello,
>
> I am trying to install gromacs 5.1.4 and getting following error of
> regression test fail.
>
> Downloading: http://gerrit.gromacs.org/download/regressiontests-5.1.
> 4.tar.gz
> -- [download 100% complete]
> CMake Error at tests/CMakeLists.txt:65 (message):
>   Download of regressiontests failed.  Expected MD5 of
>   8902358ab19343f17997d1bf85f8e69c but download has
>   3a78f965540a904c4cc1dcab1f7e0edb
>
>
> -- Configuring incomplete, errors occurred!
> See also "/home/abhishek/gromacs/gromacs-5.1.4/build/
> CMakeFiles/CMakeOutput.log".
> See also "/home/abhishek/gromacs/gromacs-5.1.4/build/
> CMakeFiles/CMakeError.log".
>
>
>
> I have tried to download regression test file from the web (
> ftp://ftp.gromacs.org/regressiontests/regressiontests-5.1.4.tar.gz) but
> this link is not working. Kindly help me to solve this issue.
>
> Thanks
>
> Abhishek
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 5 Jan 2017 17:40:44 +0900
> From: Aditya Padhi <adi.uoh at gmail.com>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Index file group selection and gmx covar error
> Message-ID:
>         <CABfSPKD=AWQydTG39HTr2ygZ+axa+NL__h83GYhmKZNc=_B3Wg@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear Gromacs users,
>
> I am trying to evaluate entropic contributions for a protein-protein
> complex using the gmx covar module and then gmx anaeig. When I directly run
> the command "gmx covar -f prod.xtc -s prod.tpr -n index.ndx -o eigenval.xvg
> -v eigenval.trr -av average.pdb -l covar.log", the program runs and
> produces the output. However, when I try to submit it into a node having 16
> cores, it shows "Illegal instruction" error and it doesn't run.
>
> In addition, when I use "qsub" to submit the job into the particular node,
> it tries to run but eventually I get an error "Fatal error: No input files
> (structure or index)". I was wondering if there is any way to specify my
> group selection (for e.g. 18 and 19) directly in my input.sh file when I
> submit using qsub and is it sufficient to make this run successful? Or the
> problem is something related to the pre-compiled binaries.
>
> If anyone can suggest a solution to this issue, it would be really helpful.
>
> Thanks,
> Aditya
>
>
> ------------------------------
>
> --
> 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.
>
> End of gromacs.org_gmx-users Digest, Vol 153, Issue 12
> ******************************************************
>



-- 
Thanks and regards


Nivedita Rai
PhD in Bioinformatics
Centre for Bioinformatics
Pondicherry University, Pondicherry (605014), INDIA