[gmx-users] gromacs.org_gmx-users Digest, Vol 154, Issue 67

João Henriques joao.henriques.32353 at gmail.com
Thu Feb 16 13:03:19 CET 2017 

Dear António,

Thank you for your reply and suggestion. It is in a way comforting to know
that someone much more intelligent and experienced than I has also
struggled with this particular issue. I was doing my best to use the native
tools distributed with gmx as much as I can, but the prohibitive amount of
time I've spent on this otherwise simple issue has driven me to abandon
this plan and make my "custom gmx gangle" with MDAnalysis. So far I am
quite impressed with this library, quite powerful indeed.

Best regards,
João


On Thu, Feb 16, 2017 at 11:42 AM, <
gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

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> Today's Topics:
>
>    1. gmx gangle (Jo?o Henriques)
>    2. Re: gmx gangle (Antonio Baptista)
>    3. Re: Regarding topology... (Dilip H N)
>    4. Doubt from topology creation using g_x2top (Rakesh Pant)
>    5. GROMACS 5.1.0 crashes on pbs queue system (Neha Gandhi)
>    6. Re: Regarding topology... (Mark Abraham)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 15 Feb 2017 20:34:20 +0100
> From: Jo?o Henriques <joao.henriques.32353 at gmail.com>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: [gmx-users] gmx gangle
> Message-ID:
>         <CALC+HGRU7SjpjQm5zxxRo6ioyhQVTb3B2F39DRv8JjhwFZn5fA at mail.gmail.
> com>
> Content-Type: text/plain; charset=UTF-8
>
> Hello everyone,
>
> It seems that my inquiries about gmx gangle and selections are either too
> funky or too basic to justify getting a single answer from the community.
> Still, I will try once more with an even simpler scenario, which will
> hopefully attract an answer (even if it's just someone telling me to stop
> reposting, despite the fact that it is not 100% a repost).
>
> I have a trajectory where the water molecules are ordered by proximity to
> the protein. I also have an index file with the N closest waters that I am
> interested in analyzing. Now, my plan is to simply compute the O-H angle
> distribution within the group composed by these N water molecules. For that
> I type something along these lines:
>
> gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -g1 vector -group1 "group
> "hydration_shell" and name OW HW1" -g2 vector -group2 "group
> "hydration_shell" and name OW HW1" -oav -oall -oh
>
> To my surprise, this command returns something completely different from
> what I expected. Instead of the angular distribution function of all pairs
> of O-H vectors from different water molecules, it outputs zero. Obviously,
> this means that the command is computing the angle between the O-H vector
> of each water molecule and itself. How can I modify my selection to produce
> the desired result?
>
> Thank you in advance,
> Best regards,
> Jo?o
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 15 Feb 2017 22:37:12 +0000 (WET)
> From: Antonio Baptista <baptista at itqb.unl.pt>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] gmx gangle
> Message-ID: <alpine.DEB.2.20.1702152232510.17090 at simul04.itqb.unl.pt>
> Content-Type: text/plain; charset="utf-8"; Format="flowed"
>
> Hi Jo?o,
>
> I used gangle to compute several angle distributions relative to the
> z-axis membrane normal, but that was almost a year ago, so I don't recall
> the details. But I can tell you that, after many failed attempts, I gave
> up from using fancy stuff in the -group1 and -group2 options. Instead, I
> ended up writing a small bash script to process one atom pair at a time
> (just one group in the .ndx file per gangle run) and to collect everything
> at the end.
>
> I understand that your problem is a bit different (your second vector is
> not an axis, but defined by a second atom pair), but maybe a similar
> "minimalist" approach could get the job done. Or not... Good luck!
>
> Best,
> Antonio
>
> On Wed, 15 Feb 2017, Jo?o Henriques wrote:
>
> > Hello everyone,
> >
> > It seems that my inquiries about gmx gangle and selections are either too
> > funky or too basic to justify getting a single answer from the community.
> > Still, I will try once more with an even simpler scenario, which will
> > hopefully attract an answer (even if it's just someone telling me to stop
> > reposting, despite the fact that it is not 100% a repost).
> >
> > I have a trajectory where the water molecules are ordered by proximity to
> > the protein. I also have an index file with the N closest waters that I
> am
> > interested in analyzing. Now, my plan is to simply compute the O-H angle
> > distribution within the group composed by these N water molecules. For
> that
> > I type something along these lines:
> >
> > gmx gangle -f xxx.xtc -s xxx.tpr -n xxx.ndx -g1 vector -group1 "group
> > "hydration_shell" and name OW HW1" -g2 vector -group2 "group
> > "hydration_shell" and name OW HW1" -oav -oall -oh
> >
> > To my surprise, this command returns something completely different from
> > what I expected. Instead of the angular distribution function of all
> pairs
> > of O-H vectors from different water molecules, it outputs zero.
> Obviously,
> > this means that the command is computing the angle between the O-H vector
> > of each water molecule and itself. How can I modify my selection to
> produce
> > the desired result?
> >
> > Thank you in advance,
> > Best regards,
> > Jo?o
> > --
> > 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.
>
> ------------------------------
>
> Message: 3
> Date: Thu, 16 Feb 2017 11:18:29 +0530
> From: Dilip H N <cy16f01.dilip at nitk.edu.in>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding topology...
> Message-ID:
>         <CAD6GXy001XCt3WkUT5fELSDEcxtx91uv6aunU6e93WZDOfRxvQ at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Can anyone help me out kindly...regarding the previous error msg tht i have
> got.....
>
>
>
>   <https://mailtrack.io/>Sent with Mailtrack
> <https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>
> On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> wrote:
>
> > Hello.. I have created a ammonia molecule... and i have CGennFF also...
> > and thn in the terminal if i type gmx pdb2gmx -f ammonia.pdb -o
> > ammonia.gro..and thn i enter for charmm36 force field...
> > and thn none for water model since i  dnt want water (i just want to
> > simulate ammonia)..
> > and i am getting again residue AMM1 is not thr i rtp file entry..
> > But Justin as u tld tht residue for ammonia is AMM1 and tht is in
> CGenFF...
> > Can u rectify me whr the fault is..??
> > below is the screen shot of both the terminal error msg and my pdb file
> > with errors..
> >
> >
> >
> >   <https://mailtrack.io/>Sent with Mailtrack
> > <https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22>
> >
> > On Tue, Feb 14, 2017 at 6:56 PM, ????? ????????? <b.mijiddorj at gmail.com>
> > wrote:
> >
> >> > ------------------------------
> >> >
> >> > Message: 6
> >> > Date: Tue, 14 Feb 2017 16:11:40 +0530
> >> > From: Dilip H N <cy16f01.dilip at nitk.edu.in>
> >> > To: gmx-users at gromacs.org
> >> > Subject: Re: [gmx-users] Regarding topology...
> >> > Message-ID:
> >> >         <CAD6GXy2oJxWPM4Qcgo_JZGVNZ1+BtpOtg5kFiX324hm2E6nr_A at mail.
> >> > gmail.com>
> >> > Content-Type: text/plain; charset=UTF-8
> >> >
> >> > How can i create a mixture of molecules and save it in .pdb format..?
> >> > Is there any softwares for tht..?? or any software for pdb generator
> for
> >> > gromacs..??
> >> > Can anybody help...??
> >> >
> >> > you can use "gmx insert-molecules" (version 5 or later) for the
> mixture,
> >> it needs pdb and topology files. you can use swissparam and prodrg
> server
> >> etc. for generating topology depending on intended force field.
> >>
> >> I don't know any special pdb generator for gromacs, because there are
> many
> >> software. what kind of system do you need?
> >>
> >> Regards,
> >> Miji
> >> --
> >> 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.
> >>
> >
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student,
> > Research Scholar,
> > Department of Chemistry,
> > National Institute of Technology-Karnataka,
> > Surathkal, Mangaluru - 575025.
> >
>
>
>
> --
> With Best Regards,
>
> DILIP.H.N
> Ph.D Student,
> Research Scholar,
> Department of Chemistry,
> National Institute of Technology-Karnataka,
> Surathkal, Mangaluru - 575025.
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 16 Feb 2017 12:02:48 +0530
> From: Rakesh Pant <rakesh.pant at students.iiserpune.ac.in>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] Doubt from topology creation using g_x2top
> Message-ID:
>         <CACqezJ6uisG60=_wUdtwcPYxodJNQby8Y58ne_exOevNdUAfsQ at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear all,
>
> I am trying to create a topology for a molecule using g_x2top and have
> defined all the atoms with connectivity in *atomname.n2t* file with
> different opls no. for all different types of atoms.
>
> But when I create topology, it does not identify all different atomtypes
> and takes one common opls no. for some of the atoms.
>
> Thanks
>
>
> Rakesh
>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 16 Feb 2017 17:50:39 +1000
> From: Neha Gandhi <n.gandhiau at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] GROMACS 5.1.0 crashes on pbs queue system
> Message-ID:
>         <CA+Hq8HwY7r+ME-+ErMGUH+SqtOxJ_VTYVtc2o0BU1-ooZs+S5w@
> mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Dear List,
>
> I have compiled gromacs 5.1.0 using MPI. The job runs interactively as well
> as through pbs submission using two nodes. However, the job crashes
> immediately when I submit more than two jobs. Below is the error:
> --------------------------------------------------------------------------
> mpirun noticed that process rank 18 with PID 153374 on node
> cl2n045.ib0.hpc.qut.edu.au exited on signal 4 (Illegal instruction).
> --------------------------------------------------------------------------
> 24 total processes killed (some possibly by mpirun during cleanup)
>
> -----
> PBS Job 1662894.pbs
> CPU time  : 00:00:34
> Wall time : 00:00:05
> Mem usage : 256kb
>
> Any input is much appreciated.
>
> --
> Regards,
> Dr. Neha S. Gandhi,
> Vice Chancellor's Research Fellow,
> Queensland University of Technology,
> 2 George Street, Brisbane, QLD 4000
> Australia
> LinkedIn
> Research Gate
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 16 Feb 2017 10:42:20 +0000
> From: Mark Abraham <mark.j.abraham at gmail.com>
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Regarding topology...
> Message-ID:
>         <CAMNuMATdDAxH5BY5o2beFhBi8PDsJ48dv9vwqi_xPH+62jR4zg at mail.
> gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi,
>
> What errors? I already helped you with some. The list can't accept
> attachments, so we can't see a screenshot. Copy and paste.
>
> Mark
>
> On Thu, 16 Feb 2017 06:49 Dilip H N <cy16f01.dilip at nitk.edu.in> wrote:
>
> > Can anyone help me out kindly...regarding the previous error msg tht i
> have
> > got.....
> >
> >
> >
> >   <https://mailtrack.io/>Sent with Mailtrack
> > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> >
> > On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N <cy16f01.dilip at nitk.edu.in>
> > wrote:
> >
> > > Hello.. I have created a ammonia molecule... and i have CGennFF also...
> > > and thn in the terminal if i type gmx pdb2gmx -f ammonia.pdb -o
> > > ammonia.gro..and thn i enter for charmm36 force field...
> > > and thn none for water model since i  dnt want water (i just want to
> > > simulate ammonia)..
> > > and i am getting again residue AMM1 is not thr i rtp file entry..
> > > But Justin as u tld tht residue for ammonia is AMM1 and tht is in
> > CGenFF...
> > > Can u rectify me whr the fault is..??
> > > below is the screen shot of both the terminal error msg and my pdb file
> > > with errors..
> > >
> > >
> > >
> > >   <https://mailtrack.io/>Sent with Mailtrack
> > > <
> > https://mailtrack.io/install?source=signature&lang=en&
> referral=cy16f01.dilip at nitk.edu.in&idSignature=22
> > >
> > >
> > > On Tue, Feb 14, 2017 at 6:56 PM, ????? ????????? <
> b.mijiddorj at gmail.com>
> > > wrote:
> > >
> > >> > ------------------------------
> > >> >
> > >> > Message: 6
> > >> > Date: Tue, 14 Feb 2017 16:11:40 +0530
> > >> > From: Dilip H N <cy16f01.dilip at nitk.edu.in>
> > >> > To: gmx-users at gromacs.org
> > >> > Subject: Re: [gmx-users] Regarding topology...
> > >> > Message-ID:
> > >> >         <CAD6GXy2oJxWPM4Qcgo_JZGVNZ1+BtpOtg5kFiX324hm2E6nr_A at mail.
> > >> > gmail.com>
> > >> > Content-Type: text/plain; charset=UTF-8
> > >> >
> > >> > How can i create a mixture of molecules and save it in .pdb
> format..?
> > >> > Is there any softwares for tht..?? or any software for pdb generator
> > for
> > >> > gromacs..??
> > >> > Can anybody help...??
> > >> >
> > >> > you can use "gmx insert-molecules" (version 5 or later) for the
> > mixture,
> > >> it needs pdb and topology files. you can use swissparam and prodrg
> > server
> > >> etc. for generating topology depending on intended force field.
> > >>
> > >> I don't know any special pdb generator for gromacs, because there are
> > many
> > >> software. what kind of system do you need?
> > >>
> > >> Regards,
> > >> Miji
> > >> --
> > >> 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.
> > >>
> > >
> > >
> > >
> > > --
> > > With Best Regards,
> > >
> > > DILIP.H.N
> > > Ph.D Student,
> > > Research Scholar,
> > > Department of Chemistry,
> > > National Institute of Technology-Karnataka,
> > > Surathkal, Mangaluru - 575025.
> > >
> >
> >
> >
> > --
> > With Best Regards,
> >
> > DILIP.H.N
> > Ph.D Student,
> > Research Scholar,
> > Department of Chemistry,
> > National Institute of Technology-Karnataka,
> > Surathkal, Mangaluru - 575025.
> > --
> > 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.
>
> End of gromacs.org_gmx-users Digest, Vol 154, Issue 67
> ******************************************************
>

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