[gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140

Sarath Chandra sarathchandradantu at gmail.com
Mon Apr 25 07:22:13 CEST 2016 

Add the following line to your .bashrc or .cshrc

source /usr/local/gromacs/bin/GMXRC

and then everytime you open a new terminal gromacs will be auto sourced.

Regards,

Sarath

-- 
Sarath Chandra Dantu, PhD, ELS
Room No. 606, New BSBE Building
Department of Biosciences and Bioengineering
Indian Institute of Technology Bombay
Powai Mumbai, 400-076, India


On 25 April 2016 at 10:35, Roshan Shrestha <roshanpra at gmail.com> wrote:

> Sorry, I found my error, should have used DGMX ...... However,  another
> problem arose after installation.  The program ran fine in that terminal by
> which I installed gromacs, but when I closed that terminal and opened
> another terminal, after typing gmx -h , it showed The program 'gmx' is
> currently not installed. You can install it by typing:
> sudo apt-get install gromacs
> I thought I properly installed gromacs, Did this problem came because I
> used
>
> source /usr/local/gromacs/bin/GMXRC
>
>
>
> On Mon, Apr 25, 2016 at 10:16 AM, Roshan Shrestha <roshanpra at gmail.com>
> wrote:
>
> > While rebuilding ,I gave the command cmake .. -GMX_USE_RDTSCP=OFF
> > But, it showed the error CMake Error: Could not create named generator
> > MX_USE_RDTSCP=OFF
> > Am I making any errors ?
> >
> > On Mon, Apr 25, 2016 at 12:18 AM, <
> > gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:
> >
> >> Send gromacs.org_gmx-users mailing list submissions to
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> >> 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. Re: Error in mdrun (Roshan Shrestha)
> >>    2. Re: Error in mdrun (Justin Lemkul)
> >>    3. Re: Graphene sheet topology (soumadwip ghosh)
> >>    4. Re: Gromacs-5.1.2 Checkpoint/restart example (Husen R)
> >>    5. how to convert CHARMM36 system into virtual site system? (Albert)
> >>    6. g_helix (leila salimi)
> >>
> >>
> >> ----------------------------------------------------------------------
> >>
> >> Message: 1
> >> Date: Sun, 24 Apr 2016 17:51:58 +0545
> >> From: Roshan Shrestha <roshanpra at gmail.com>
> >> To: gromacs.org_gmx-users at maillist.sys.kth.se
> >> Subject: Re: [gmx-users] Error in mdrun
> >> Message-ID:
> >>         <
> >> CAGE0GtR3Wn0xEVdwm+hbuD0U5MJpROcm4OPLX6oDjKLTMLXQSQ at mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> How to turn off that option ? I mean, the error cam up when I typed
> >>
> >> gmx mdrun -deffnm em -v
> >>
> >> So, what should command I use to turn off that option. Thanks
> >>
> >>
> >> On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha <roshanpra at gmail.com>
> >> wrote:
> >>
> >> > My CPU configuration is rather too old,
> >> > Architecture:          i686
> >> > CPU op-mode(s):        32-bit, 64-bit
> >> > Byte Order:            Little Endian
> >> > CPU(s):                2
> >> > On-line CPU(s) list:   0,1
> >> > Thread(s) per core:    1
> >> > Core(s) per socket:    2
> >> > Socket(s):             1
> >> > Vendor ID:             GenuineIntel
> >> > CPU family:            6
> >> > Model:                 15
> >> > Model name:            Intel(R) Core(TM)2 Duo CPU     E6750  @ 2.66GHz
> >> > Stepping:              11
> >> > CPU MHz:               2003.000
> >> > CPU max MHz:           2670.0000
> >> > CPU min MHz:           2003.0000
> >> > BogoMIPS:              5333.10
> >> > Virtualization:        VT-x
> >> > L1d cache:             32K
> >> > L1i cache:             32K
> >> > L2 cache:              4096K
> >> > I installed Gromacs 5.0.6, but while running mdrun, I got the error:
> >> > Program gmx, VERSION 5.0.6
> >> > Source code file:
> >> >
> >>
> /build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
> >> > line: 212
> >> >
> >> > Fatal error:
> >> > The gmx executable was compiled to use the rdtscp CPU instruction.
> >> > However, this is not supported by the current hardware and continuing
> >> would
> >> > lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF
> >> CMake
> >> > option.
> >> > For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> > website at http://www.gromacs.org/Documentation/Errors
> >> >
> >> > How to solve this problem ? Thanks.
> >> >
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 2
> >> Date: Sun, 24 Apr 2016 08:08:59 -0400
> >> From: Justin Lemkul <jalemkul at vt.edu>
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Error in mdrun
> >> Message-ID: <571CB75B.7060608 at vt.edu>
> >> Content-Type: text/plain; charset=windows-1252; format=flowed
> >>
> >>
> >>
> >> On 4/24/16 8:06 AM, Roshan Shrestha wrote:
> >> > How to turn off that option ? I mean, the error cam up when I typed
> >> >
> >> > gmx mdrun -deffnm em -v
> >> >
> >> > So, what should command I use to turn off that option. Thanks
> >> >
> >>
> >> "Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF CMake option."
> >>
> >> You have to re-compile and re-install.
> >>
> >> -Justin
> >>
> >> >
> >> > On Sun, Apr 24, 2016 at 5:00 PM, Roshan Shrestha <roshanpra at gmail.com
> >
> >> > wrote:
> >> >
> >> >> My CPU configuration is rather too old,
> >> >> Architecture:          i686
> >> >> CPU op-mode(s):        32-bit, 64-bit
> >> >> Byte Order:            Little Endian
> >> >> CPU(s):                2
> >> >> On-line CPU(s) list:   0,1
> >> >> Thread(s) per core:    1
> >> >> Core(s) per socket:    2
> >> >> Socket(s):             1
> >> >> Vendor ID:             GenuineIntel
> >> >> CPU family:            6
> >> >> Model:                 15
> >> >> Model name:            Intel(R) Core(TM)2 Duo CPU     E6750  @
> 2.66GHz
> >> >> Stepping:              11
> >> >> CPU MHz:               2003.000
> >> >> CPU max MHz:           2670.0000
> >> >> CPU min MHz:           2003.0000
> >> >> BogoMIPS:              5333.10
> >> >> Virtualization:        VT-x
> >> >> L1d cache:             32K
> >> >> L1i cache:             32K
> >> >> L2 cache:              4096K
> >> >> I installed Gromacs 5.0.6, but while running mdrun, I got the error:
> >> >> Program gmx, VERSION 5.0.6
> >> >> Source code file:
> >> >>
> >>
> /build/gromacs-yTV9IQ/gromacs-5.0.6/src/gromacs/gmxlib/gmx_detect_hardware.c,
> >> >> line: 212
> >> >>
> >> >> Fatal error:
> >> >> The gmx executable was compiled to use the rdtscp CPU instruction.
> >> >> However, this is not supported by the current hardware and continuing
> >> would
> >> >> lead to a crash. Please rebuild GROMACS with the GMX_USE_RDTSCP=OFF
> >> CMake
> >> >> option.
> >> >> For more information and tips for troubleshooting, please check the
> >> GROMACS
> >> >> website at http://www.gromacs.org/Documentation/Errors
> >> >>
> >> >> How to solve this problem ? Thanks.
> >> >>
> >>
> >> --
> >> ==================================================
> >>
> >> Justin A. Lemkul, Ph.D.
> >> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>
> >> Department of Pharmaceutical Sciences
> >> School of Pharmacy
> >> Health Sciences Facility II, Room 629
> >> University of Maryland, Baltimore
> >> 20 Penn St.
> >> Baltimore, MD 21201
> >>
> >> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> http://mackerell.umaryland.edu/~jalemkul
> >>
> >> ==================================================
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 3
> >> Date: Sun, 24 Apr 2016 18:18:10 +0530
> >> From: soumadwip ghosh <soumadwipghosh at gmail.com>
> >> To: "gromacs.org_gmx-users"
> >>         <gromacs.org_gmx-users at maillist.sys.kth.se>
> >> Subject: Re: [gmx-users] Graphene sheet topology
> >> Message-ID:
> >>         <
> >> CAOci0DaVK+ghHjcb4yy5AGtLcCCr+BkL+4kWfT13xxDx8V_+dQ at mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> Thanks Justin as always for your prompt reply.
> >>
> >> I have now created the graphene topology the way u suggested that is I
> >> issued the following command
> >>
> >> 1. g_x2top -f file.gro -o graphene.top -pbc: I did not prefer to use the
> >> -noparam option since it does not print the k0, k1 and similar values.
> >>
> >> 2. I have now started the simulation with all my mdp files (ions.mdp,
> >> minim.mdp, nvt.mdp, npt.mdp and md.mdp) containing the "periodic
> >> molecules=yes" line and as of now the simulation is running fine. But
> the
> >> last one crashed around 25 ns showing the Lincs warnings and stuffs so
> >> keeping my fingers crossed.
> >>
> >> 3. I am keeping the dihedral function type 1 as per your suggestion.
> >>
> >> Please let me know if what I am doing right now as mentioned above makes
> >> sense or not. I will update on the outcomes of my simulation even if
> >> everything goes right.
> >>
> >>
> >> Thanks once again for the reply Justin..:)
> >>
> >> Soumadwip Ghosh
> >> Senior Research Fellow
> >> Indian Institute of Technology Bombay
> >> India
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 4
> >> Date: Sun, 24 Apr 2016 19:57:58 +0700
> >> From: Husen R <hus3nr at gmail.com>
> >> To: gmx-users at gromacs.org
> >> Subject: Re: [gmx-users] Gromacs-5.1.2 Checkpoint/restart example
> >> Message-ID:
> >>         <CACPfdUuTa5Cq8_5n3q7e=
> >> CHaRSU2A5XzitcO3cf5HKKQs+a4sw at mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> Hi,
> >>
> >> Thanks a lot !
> >> I'll try it,..
> >>
> >> Regards,
> >>
> >>
> >> Husen
> >>
> >> On Sun, Apr 24, 2016 at 6:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >> >
> >> >
> >> > On 4/24/16 12:04 AM, Husen R wrote:
> >> >
> >> >> Dear all,
> >> >>
> >> >> is there any complete documentation discussing checkpoint/restart in
> >> >> Gromacs-5.1.2 ?
> >> >> I found this link that discuss checkpoint (
> >> >> http://www.gromacs.org/Documentation/How-tos/Extending_Simulations)
> >> and
> >> >> this link that discuss restart (
> >> >> http://www.gromacs.org/Documentation/How-tos/Doing_Restarts) but
> these
> >> >> are
> >> >> not specifically for gromacs 5.1.2.
> >> >>
> >> >>
> >> > There are no differences for 5.1.2, so that information is all
> relevant.
> >> >
> >> > -Justin
> >> >
> >> > --
> >> > ==================================================
> >> >
> >> > Justin A. Lemkul, Ph.D.
> >> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >> >
> >> > Department of Pharmaceutical Sciences
> >> > School of Pharmacy
> >> > Health Sciences Facility II, Room 629
> >> > University of Maryland, Baltimore
> >> > 20 Penn St.
> >> > Baltimore, MD 21201
> >> >
> >> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >> > http://mackerell.umaryland.edu/~jalemkul
> >> >
> >> > ==================================================
> >> > --
> >> > 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: 5
> >> Date: Sun, 24 Apr 2016 20:19:01 +0200
> >> From: Albert <mailmd2011 at gmail.com>
> >> To: gmx-users at gromacs.org
> >> Subject: [gmx-users] how to convert CHARMM36 system into virtual site
> >>         system?
> >> Message-ID: <571D0E15.1080202 at gmail.com>
> >> Content-Type: text/plain; charset=utf-8; format=flowed
> >>
> >> Hello:
> >>
> >> I've built a membrane system from CHARMM-GUI with CHARMM36 FF. I am just
> >> wondering how can we convert the lipids molecule to virtual site lipids?
> >>
> >> Thank you very much
> >>
> >> Albert
> >>
> >>
> >> ------------------------------
> >>
> >> Message: 6
> >> Date: Sun, 24 Apr 2016 20:33:46 +0200
> >> From: leila salimi <leilasalimi at gmail.com>
> >> To: gmx-users at gromacs.org
> >> Subject: [gmx-users] g_helix
> >> Message-ID:
> >>         <
> >> CAFesFkthKSS_-oBi4A-KYK4dMQvLMzNOSFwpbNhdk7AYt1vUSg at mail.gmail.com>
> >> Content-Type: text/plain; charset=UTF-8
> >>
> >> Dear all,
> >>
> >> I have a question regarding to calculate g_helix, I am not sure about
> the
> >> index numbers for using g_helix!
> >> Should I use the all atom numbers of protein that I have? If not please
> >> explain to me which indexes of protein I have to choose.
> >>
> >> The same for do_dssp, I have to use the all atom numbers of protein or
> the
> >> residue numbers of protein!
> >>
> >> Thanks in advance,
> >> Leila
> >>
> >>
> >> ------------------------------
> >>
> >> --
> >> Gromacs Users mailing list
> >>
> >> * Please search the archive at
> >> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> >> posting!
> >>
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> >>
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> >> 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 144, Issue 140
> >> *******************************************************
> >>
> >
> >
> --
> Gromacs Users mailing list
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