[gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140
Roshan Shrestha
roshanpra at gmail.com
Mon Apr 25 06:32:07 CEST 2016
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:
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> 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!
> >
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> >
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> > 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
>
>
> ------------------------------
>
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