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-requ...@maillist.sys.kth.se> wrote: > Send gromacs.org_gmx-users mailing list submissions to > gromacs.org_gmx-users@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-requ...@maillist.sys.kth.se > > You can reach the person managing the list at > gromacs.org_gmx-users-ow...@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. 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.32...@gmail.com> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: [gmx-users] gmx gangle > Message-ID: > <CALC+HGRU7SjpjQm5zxxRo6ioyhQVTb3B2F39DRv8JjhwFZn5fA@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 <bapti...@itqb.unl.pt> > To: Discussion list for GROMACS users <gmx-us...@gromacs.org> > Subject: Re: [gmx-users] gmx gangle > Message-ID: <alpine.deb.2.20.1702152232510.17...@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-requ...@gromacs.org. > > ------------------------------ > > Message: 3 > Date: Thu, 16 Feb 2017 11:18:29 +0530 > From: Dilip H N <cy16f01.di...@nitk.edu.in> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding topology... > Message-ID: > <CAD6GXy001XCt3WkUT5fELSDEcxtx91uv6aunU6e93WZDOfRxvQ@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.di...@nitk.edu.in&idSignature=22> > > On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N <cy16f01.di...@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.di...@nitk.edu.in&idSignature=22> > > > > On Tue, Feb 14, 2017 at 6:56 PM, ????? ????????? <b.mijidd...@gmail.com> > > wrote: > > > >> > ------------------------------ > >> > > >> > Message: 6 > >> > Date: Tue, 14 Feb 2017 16:11:40 +0530 > >> > From: Dilip H N <cy16f01.di...@nitk.edu.in> > >> > To: gmx-us...@gromacs.org > >> > Subject: Re: [gmx-users] Regarding topology... > >> > Message-ID: > >> > <CAD6GXy2oJxWPM4Qcgo_JZGVNZ1+BtpOtg5kFiX324hm2E6nr_A@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-requ...@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.p...@students.iiserpune.ac.in> > To: gromacs.org_gmx-users@maillist.sys.kth.se > Subject: [gmx-users] Doubt from topology creation using g_x2top > Message-ID: > <CACqezJ6uisG60=_wUdtwcPYxodJNQby8Y58ne_exOevNdUAfsQ@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.gandh...@gmail.com> > To: gromacs.org_gmx-users@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.abra...@gmail.com> > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Regarding topology... > Message-ID: > <CAMNuMATdDAxH5BY5o2beFhBi8PDsJ48dv9vwqi_xPH+62jR4zg@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.di...@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.di...@nitk.edu.in&idSignature=22 > > > > > > > On Wed, Feb 15, 2017 at 4:56 PM, Dilip H N <cy16f01.di...@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.di...@nitk.edu.in&idSignature=22 > > > > > > > > > On Tue, Feb 14, 2017 at 6:56 PM, ????? ????????? < > b.mijidd...@gmail.com> > > > wrote: > > > > > >> > ------------------------------ > > >> > > > >> > Message: 6 > > >> > Date: Tue, 14 Feb 2017 16:11:40 +0530 > > >> > From: Dilip H N <cy16f01.di...@nitk.edu.in> > > >> > To: gmx-us...@gromacs.org > > >> > Subject: Re: [gmx-users] Regarding topology... > > >> > Message-ID: > > >> > <CAD6GXy2oJxWPM4Qcgo_JZGVNZ1+BtpOtg5kFiX324hm2E6nr_A@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-requ...@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-requ...@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-requ...@gromacs.org. > > End of gromacs.org_gmx-users Digest, Vol 154, Issue 67 > ****************************************************** > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? 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