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

2016-04-24 Thread Sarath Chandra 
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  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 
> 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-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. 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 
> >> To: gromacs.org_gmx-users@maillist.sys.kth.se
> >> Subject: Re: [gmx-users] Error in mdrun
> >> Message-ID:
> >> <
> >> cage0gtr3wn0xevdwm+hbud0u5mjprocm4oplx6odjkltmlx...@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 
> >> 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.
> >> > CPU min MHz:   2003.
> >> > 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 
> >> To: gmx-us...@gromacs.org
> >> Subject: Re: [gmx-users] Error in mdrun
> >> Message-ID: <571cb75b.7060...@vt.edu>
> >> Content-Type: text/plain; charset=windows-1252;

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

2016-04-24 Thread Roshan Shrestha 
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 
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-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. 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 
>> To: gromacs.org_gmx-users@maillist.sys.kth.se
>> Subject: Re: [gmx-users] Error in mdrun
>> Message-ID:
>> <
>> cage0gtr3wn0xevdwm+hbud0u5mjprocm4oplx6odjkltmlx...@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 
>> 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.
>> > CPU min MHz:   2003.
>> > 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 
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Error in mdrun
>> Message-ID: <571cb75b.7060...@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 
>> > 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
>>

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

2016-04-24 Thread Roshan Shrestha 
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-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. 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 
> To: gromacs.org_gmx-users@maillist.sys.kth.se
> Subject: Re: [gmx-users] Error in mdrun
> Message-ID:
> <
> cage0gtr3wn0xevdwm+hbud0u5mjprocm4oplx6odjkltmlx...@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 
> 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.
> > CPU min MHz:   2003.
> > 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 
> To: gmx-us...@gromacs.org
> Subject: Re: [gmx-users] Error in mdrun
> Message-ID: <571cb75b.7060...@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 
> > 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.
> >> CPU min MHz:   2003.
> >> 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