[gmx-users] gromacs.org_gmx-users Digest, Vol 144, Issue 140
Roshan Shrestha
roshanpra at gmail.com
Mon Apr 25 07:05:50 CEST 2016
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:
>
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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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>> >
>>
>>
>> ------------------------------
>>
>> 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
>>
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>> End of gromacs.org_gmx-users Digest, Vol 144, Issue 140
>> *******************************************************
>>
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