Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Roland Schulz]

I recommend to use Linux inside a Virtualbox (http://www.virtualbox.org/)
over Cygwin. Cygwin is rather slow.

We should have a Virtual Appliance with GROMACS installed ...

On Tue, Oct 5, 2010 at 11:42 PM, Justin A. Lemkul  wrote:

>
>
> #ZHAO LINA# wrote:
>
>> sudo apt-get install grace
>>
>
> For Linux sure, but I think the Cygwin equivalent is something like cyg-get
> (which is probably not standard) and there may or may not be a "grace"
> package available.
>
> -Justin
>
>
>
>> 
>> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
>> behalf of Justin A. Lemkul [jalem...@vt.edu]
>> Sent: Wednesday, October 06, 2010 11:29 AM
>> To: Gromacs Users' List
>> Subject: Re: [gmx-users] Re : installation of gromacs in windows on cygwin
>>
>> bharat gupta wrote:
>>
>>> thanks for ur help.. I have figured out the problem and not installation
>>> is going on .. I want to know one more thing that xmgrace which is
>>> required for plotting the data .. how can we install it as I have
>>> searched on google .. but  I am not able to get the correct link
>>>
>>>
>> The first Google result for "xmgrace" is the site you want, I don't know
>> what
>> else to tell you.
>>
>> http://plasma-gate.weizmann.ac.il/Grace/
>>
>> Follow whatever documentation they provide to install it.
>>
>> -Justin
>>
>>  --
>>> Bharat
>>> Ph.D. Candidate
>>> Room No. : 7202A, 2nd Floor
>>> Biomolecular Engineering Laboratory
>>> Division of Chemical Engineering and Polymer Science
>>> Pusan National University
>>> Busan -609735
>>> South Korea
>>> Lab phone no. - +82-51-510-3680, +82-51-583-8343
>>> Mobile no. - 010-5818-3680
>>> E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
>>>
>>>
>> --
>> 
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>> 
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
> --
> 
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> 
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the www interface
> or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

#ZHAO LINA# wrote:

sudo apt-get install grace


For Linux sure, but I think the Cygwin equivalent is something like cyg-get 
(which is probably not standard) and there may or may not be a "grace" package 
available.


-Justin




From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, October 06, 2010 11:29 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] Re : installation of gromacs in windows on cygwin

bharat gupta wrote:

thanks for ur help.. I have figured out the problem and not installation
is going on .. I want to know one more thing that xmgrace which is
required for plotting the data .. how can we install it as I have
searched on google .. but  I am not able to get the correct link



The first Google result for "xmgrace" is the site you want, I don't know what
else to tell you.

http://plasma-gate.weizmann.ac.il/Grace/

Follow whatever documentation they provide to install it.

-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
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RE: [gmx-users] Re : installation of gromacs in windows on cygwin

[#ZHAO LINA#]

sudo apt-get install grace


From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf 
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Wednesday, October 06, 2010 11:29 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] Re : installation of gromacs in windows on cygwin

bharat gupta wrote:
> thanks for ur help.. I have figured out the problem and not installation
> is going on .. I want to know one more thing that xmgrace which is
> required for plotting the data .. how can we install it as I have
> searched on google .. but  I am not able to get the correct link
>

The first Google result for "xmgrace" is the site you want, I don't know what
else to tell you.

http://plasma-gate.weizmann.ac.il/Grace/

Follow whatever documentation they provide to install it.

-Justin

> --
> Bharat
> Ph.D. Candidate
> Room No. : 7202A, 2nd Floor
> Biomolecular Engineering Laboratory
> Division of Chemical Engineering and Polymer Science
> Pusan National University
> Busan -609735
> South Korea
> Lab phone no. - +82-51-510-3680, +82-51-583-8343
> Mobile no. - 010-5818-3680
> E-mail : monu46...@yahoo.com <mailto:monu46...@yahoo.com>
>

--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

bharat gupta wrote:
thanks for ur help.. I have figured out the problem and not installation 
is going on .. I want to know one more thing that xmgrace which is 
required for plotting the data .. how can we install it as I have 
searched on google .. but  I am not able to get the correct link 



The first Google result for "xmgrace" is the site you want, I don't know what 
else to tell you.


http://plasma-gate.weizmann.ac.il/Grace/

Follow whatever documentation they provide to install it.

-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[bharat gupta]

thanks for ur help.. I have figured out the problem and not installation is
going on .. I want to know one more thing that xmgrace which is required for
plotting the data .. how can we install it as I have searched on google ..
but  I am not able to get the correct link

-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

bharat gupta wrote:


build type ?? ... actually I am new to cygwin so I don't know .. what 
exactly do I have to do for this one ??


If you installed FFTW, then its configure script must have properly detected 
your build type.  Check the config.log from that process to see what it used. 
It is weird that Gromacs can't detect it, though.


-Justin


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[bharat gupta]

build type ?? ... actually I am new to cygwin so I don't know .. what
exactly do I have to do for this one ??
-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists

Re: [gmx-users] Re : installation of gromacs in windows on cygwin

[Justin A. Lemkul]

bharat gupta wrote:

Hi all

I am trying installing gromacs 4.5.1 in windows using cygwin .. I have 
fftw3 package also without any error.. but the moment I use ./configure 
command given in the installation instruction I am getting the following 
error :-



se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure
checking build system type... config/config.guess: line 136:  4000 Aborted
   ( test -f /.attbin/uname ) > /dev/null 2>&1
config/config.guess: line 1308:  3184 Aborted ( umask 
077 && mkd

ir $tmp )
config/config.guess: line 1308:  4060 Aborted ( umask 
077 && mkd

ir $tmp )
config.guess: cannot create a temporary directory in /tmp
config/config.guess: line 1308:  3248 Aborted ( rm -f 
$tmpfiles

2> /dev/null; rmdir $tmp 2> /dev/null )
configure: error: cannot guess build type; you must specify one

se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure --enable-shared LDFLAGS = '-L/usr/local/lib'
configure: WARNING: you should use --build, --host, --target
configure: error: invalid variable name: `'



There should not be spaces within the declaration of LDFLAGS, i.e.:

LDFLAGS='-L/usr/local/lib'

You are also being told that configure cannot guess your build type, so it must 
be specified manually.


-Justin



Can anybody help me out in this regard ...


--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com 



--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
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[gmx-users] Re : installation of gromacs in windows on cygwin

[bharat gupta]

Hi all

I am trying installing gromacs 4.5.1 in windows using cygwin .. I have fftw3
package also without any error.. but the moment I use ./configure command
given in the installation instruction I am getting the following error :-


se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure
checking build system type... config/config.guess: line 136:  4000 Aborted
   ( test -f /.attbin/uname ) > /dev/null 2>&1
config/config.guess: line 1308:  3184 Aborted ( umask 077 &&
mkd
ir $tmp )
config/config.guess: line 1308:  4060 Aborted ( umask 077 &&
mkd
ir $tmp )
config.guess: cannot create a temporary directory in /tmp
config/config.guess: line 1308:  3248 Aborted ( rm -f
$tmpfiles
2> /dev/null; rmdir $tmp 2> /dev/null )
configure: error: cannot guess build type; you must specify one

se...@selva-pc /fftw-3.2.2/gromacs-4.5.1
$ ./configure --enable-shared LDFLAGS = '-L/usr/local/lib'
configure: WARNING: you should use --build, --host, --target
configure: error: invalid variable name: `'


Can anybody help me out in this regard ...


-- 
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd Floor
Biomolecular Engineering Laboratory
Division of Chemical Engineering and Polymer Science
Pusan National University
Busan -609735
South Korea
Lab phone no. - +82-51-510-3680, +82-51-583-8343
Mobile no. - 010-5818-3680
E-mail : monu46...@yahoo.com
-- 
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at 
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the 
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Can't post? Read http://www.gromacs.org/Support/Mailing_Lists