Re: [gmx-users] Installation Problem... No command 'gmx' found

[Md. Imrul Reza Shishir]

Thanks everyone. For your quick reply and support.

On Thu, Apr 21, 2016 at 10:37 PM, Justin Lemkul <jalem...@vt.edu> wrote:

>
>
> On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:
>
>> Hi, in my case gmx is only needed for certain commands. For example
>> pdb2gmx is working if I use it solo, not with gmx. It's worth a shot.
>>
>>
> This is true for versions in the 5.0.x series; they can be called via gmx
> or through the old syntax without it because the commands are all installed
> as links to gmx.  In 5.1.x this will not work; gmx/gmx_mpi (depending on
> the installation) is mandatory.
>
> -Justin
>
>
> 
>> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
>> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email
>> Gmail Pribadi <hus...@gmail.com>
>> Sent: Thursday, April 21, 2016 9:18 AM
>> To: gmx-us...@gromacs.org
>> Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found
>>
>> Hi,
>>
>> Try gmx [command] . Ex. gmx mdrun -option
>>
>> Regards,
>>
>>
>> Husen
>>
>> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
>>>
>>> Hi,
>>>
>>> Try gmx_mpi.
>>>
>>> Regards
>>> Terry
>>>
>>>
>>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir <
>>>> imrul.reza.shis...@gmail.com> wrote:
>>>>
>>>> Dear all user
>>>>
>>>> I install gromacs in my laptop its perfectly ok. But i have problem to
>>>> install in my desktop there i face problem.
>>>> In my desktop i want to compile with cuda accelerator and MPI option. I
>>>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>>>> this driver is ok.
>>>>
>>>> For gromacs i run this installation command.
>>>>
>>>> tar -xzvf gromacs-5.1.2.tar.gz
>>>> cd gromacs-5.1.2.tar.gz
>>>> mkdir build
>>>> cd build
>>>> CMAKE  -DGMX_BUILD_OWN_FFTW=on
>>>> -DGMX_GPU=on
>>>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>>>> make -j16
>>>> make check
>>>> sudo make install -j16
>>>>
>>>> source /usr/local/gromacs/bin/GMXRC
>>>>
>>>> In the installation procedure i dont find any error. All 26 test
>>>> completed
>>>> without error.
>>>>
>>>> But when i try to run "gmx or gmx help"
>>>>
>>>> There is error no command gmx found. I need your guidance.
>>>>
>>>> Best Regards
>>>>
>>>> --
>>>> *Md Imrul Reza Shishir*
>>>> --
>>>> 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
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>>> posting!
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>>> send a mail to gmx-users-requ...@gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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>> posting!
>>
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>> send a mail to gmx-users-requ...@gromacs.org.
>>
>>
> --
> ==
>
> 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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
>
> --
> Gromacs Users mailing list
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> * Please search the archive at
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> posting!
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> send a mail to gmx-users-requ...@gromacs.org.
>



-- 
*Md Imrul Reza Shishir*
Master Student
*Inha University*
*CRC for NanoCellulose Future Composites*
36 Getbeol-ro, Yeonsu-gu
Incheon 21999
South Korea
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[Justin Lemkul]

On 4/21/16 9:35 AM, Sotirios Dionysios I. Papadatos wrote:

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is 
working if I use it solo, not with gmx. It's worth a shot.



This is true for versions in the 5.0.x series; they can be called via gmx or 
through the old syntax without it because the commands are all installed as 
links to gmx.  In 5.1.x this will not work; gmx/gmx_mpi (depending on the 
installation) is mandatory.


-Justin



From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email Gmail Pribadi 
<hus...@gmail.com>
Sent: Thursday, April 21, 2016 9:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen


On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:

Hi,

Try gmx_mpi.

Regards
Terry



On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
<imrul.reza.shis...@gmail.com> wrote:

Dear all user

I install gromacs in my laptop its perfectly ok. But i have problem to
install in my desktop there i face problem.
In my desktop i want to compile with cuda accelerator and MPI option. I
install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
this driver is ok.

For gromacs i run this installation command.

tar -xzvf gromacs-5.1.2.tar.gz
cd gromacs-5.1.2.tar.gz
mkdir build
cd build
CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
-DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
make -j16
make check
sudo make install -j16

source /usr/local/gromacs/bin/GMXRC

In the installation procedure i dont find any error. All 26 test completed
without error.

But when i try to run "gmx or gmx help"

There is error no command gmx found. I need your guidance.

Best Regards

--
*Md Imrul Reza Shishir*
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--
==

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[Sotirios Dionysios I. Papadatos]

Hi, in my case gmx is only needed for certain commands. For example pdb2gmx is 
working if I use it solo, not with gmx. It's worth a shot.


From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se 
<gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Email Gmail 
Pribadi <hus...@gmail.com>
Sent: Thursday, April 21, 2016 9:18 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] Installation Problem... No command 'gmx' found

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen

> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
>
> Hi,
>
> Try gmx_mpi.
>
> Regards
> Terry
>
>
>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>> <imrul.reza.shis...@gmail.com> wrote:
>>
>> Dear all user
>>
>> I install gromacs in my laptop its perfectly ok. But i have problem to
>> install in my desktop there i face problem.
>> In my desktop i want to compile with cuda accelerator and MPI option. I
>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>> this driver is ok.
>>
>> For gromacs i run this installation command.
>>
>> tar -xzvf gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2.tar.gz
>> mkdir build
>> cd build
>> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>> make -j16
>> make check
>> sudo make install -j16
>>
>> source /usr/local/gromacs/bin/GMXRC
>>
>> In the installation procedure i dont find any error. All 26 test completed
>> without error.
>>
>> But when i try to run "gmx or gmx help"
>>
>> There is error no command gmx found. I need your guidance.
>>
>> Best Regards
>>
>> --
>> *Md Imrul Reza Shishir*
>> --
>> 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
>
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> mail to gmx-users-requ...@gromacs.org.
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Re: [gmx-users] Installation Problem... No command 'gmx' found

[Email Gmail Pribadi]

Hi,

Try gmx [command] . Ex. gmx mdrun -option

Regards,


Husen

> On 21 Apr 2016, at 12.31, terrence...@gmail.com wrote:
> 
> Hi, 
> 
> Try gmx_mpi.
> 
> Regards
> Terry
> 
> 
>> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>>  wrote:
>> 
>> Dear all user
>> 
>> I install gromacs in my laptop its perfectly ok. But i have problem to
>> install in my desktop there i face problem.
>> In my desktop i want to compile with cuda accelerator and MPI option. I
>> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
>> this driver is ok.
>> 
>> For gromacs i run this installation command.
>> 
>> tar -xzvf gromacs-5.1.2.tar.gz
>> cd gromacs-5.1.2.tar.gz
>> mkdir build
>> cd build
>> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
>> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
>> make -j16
>> make check
>> sudo make install -j16
>> 
>> source /usr/local/gromacs/bin/GMXRC
>> 
>> In the installation procedure i dont find any error. All 26 test completed
>> without error.
>> 
>> But when i try to run "gmx or gmx help"
>> 
>> There is error no command gmx found. I need your guidance.
>> 
>> Best Regards
>> 
>> -- 
>> *Md Imrul Reza Shishir*
>> -- 
>> 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.
> -- 
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> 
> * 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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Re: [gmx-users] Installation Problem... No command 'gmx' found

[terrencesun]

Hi, 

Try gmx_mpi.

Regards
Terry


> On 21 Apr 2016, at 12:11 PM, Md. Imrul Reza Shishir 
>  wrote:
> 
> Dear all user
> 
> I install gromacs in my laptop its perfectly ok. But i have problem to
> install in my desktop there i face problem.
> In my desktop i want to compile with cuda accelerator and MPI option. I
> install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
> this driver is ok.
> 
> For gromacs i run this installation command.
> 
> tar -xzvf gromacs-5.1.2.tar.gz
> cd gromacs-5.1.2.tar.gz
> mkdir build
> cd build
> CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
> -DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
> make -j16
> make check
> sudo make install -j16
> 
> source /usr/local/gromacs/bin/GMXRC
> 
> In the installation procedure i dont find any error. All 26 test completed
> without error.
> 
> But when i try to run "gmx or gmx help"
> 
> There is error no command gmx found. I need your guidance.
> 
> Best Regards
> 
> -- 
> *Md Imrul Reza Shishir*
> -- 
> 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.
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[gmx-users] Installation Problem... No command 'gmx' found

[Md. Imrul Reza Shishir]

Dear all user

I install gromacs in my laptop its perfectly ok. But i have problem to
install in my desktop there i face problem.
In my desktop i want to compile with cuda accelerator and MPI option. I
install successfully openmpi-1.10.2 and cuda-7.5 with nvidia driver. all
this driver is ok.

For gromacs i run this installation command.

tar -xzvf gromacs-5.1.2.tar.gz
cd gromacs-5.1.2.tar.gz
mkdir build
cd build
CMAKE  -DGMX_BUILD_OWN_FFTW=on -DGMX_GPU=on
-DGMX_MPI=on -DREGRESSIONTEST_DOWNLOAD=on
make -j16
make check
sudo make install -j16

source /usr/local/gromacs/bin/GMXRC

In the installation procedure i dont find any error. All 26 test completed
without error.

But when i try to run "gmx or gmx help"

There is error no command gmx found. I need your guidance.

​Best Regards

-- 
*Md Imrul Reza Shishir*
-- 
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

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