[gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1

2008-09-16 Thread Vitaly Chaban 
>> I am a beginner for Gromacs. I am using the latest version  Gromacs 4.0
>> beta1. Then I follow the tutorial part: Introduction to MD 
>>  by the Groningen group. 
>> Compiling is ok, but I always get the Segmentation fault when I use 
>> command : genbox -cp minimized_box.gro -cs spc216.gro -o 
>> minimized_water.gro -p aki.top. Also I get the same problem when i try 
>> other exercises.  Does anyone has same problem like me ? or can anyone
>> give me a hint for that?  Thanks in advance. 
> 
> It sounds like your installation is faulty.  What architecture are you 
> running 
> on?  What compilers did you use?
> 
> If you are just starting out, it is probably better to use an official 
> release 
> of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development.
> 
> -Justin

Justin,
A few days ago I experienced the same problem with genbox in gmx-4.0-beta. I 
didn't
pay much attention to it since it's just CVS but it actually was
permanently present. gmx-4.0 compiled with the same parameters on the same 
system does not
give this error.

Xianghong,
There's no such problem in gmx-3.3.3 and earlier ones. I would suggest
you to use them to avoid much headache.


-- 
Vitaly V. Chaban
School of Chemistry
National University of Kharkiv
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: [EMAIL PROTECTED]
skype: vvchaban
tel.: +38-097-8259698

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Re: [gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1

2008-09-16 Thread Justin A. Lemkul 



Justin A. Lemkul wrote:



xianghong qi wrote:

Thanks for your response.
I followed the instruction in CVS. my architecture is x86-64, and 
compiler is gcc.  thanks.


Be careful to use a compatible gcc version (i.e., not 4.1.x).  Bad
compilers can often produce nonfunctional executables.

-Justin


I will try 3.3.3
-Xianghong Qi

On Tue, Sep 16, 2008 at 4:02 PM, Justin A. Lemkul <[EMAIL PROTECTED] 
> wrote:




xianghong qi wrote:

Hi, everyone:

I am a beginner for Gromacs. I am using the latest version
 Gromacs 4.0 beta1. Then I follow the tutorial part:
Introduction to MD 
by the Groningen group. Compiling is ok, but I always get the
Segmentation fault when I use command : genbox -cp
minimized_box.gro -cs spc216.gro -o minimized_water.gro -p
aki.top. Also I get the same problem when i try other exercises.
 Does anyone has same problem like me ? or can anyone

give me a hint for that?  Thanks in advance.


It sounds like your installation is faulty.  What architecture are
you running on?  What compilers did you use?

If you are just starting out, it is probably better to use an
official release of Gromacs (the latest being 3.3.3), since 4.0beta1
is still in development.

-Justin


-Xianghong Qi

-- Postdoctoral Associate
Department of Chemistry
University of Pittsburgh
Chevron Science Center
219 Parkman Avenue
Pittsburgh, PA 15260
Office: 338 EBERLY
Phone: 412-383-5400


Some people make the world more special just by being in it.






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-- 

Justin A. Lemkul
Graduate Research Assistant
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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--
Postdoctoral Associate
Department of Chemistry
University of Pittsburgh
Chevron Science Center
219 Parkman Avenue
Pittsburgh, PA 15260
Office: 338 EBERLY
Phone: 412-383-5400


Some people make the world more special just by being in it.




--


Justin A. Lemkul
Graduate Research Assistant
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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Re: [gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1

2008-09-16 Thread xianghong qi 
Thanks for your response.
I followed the instruction in CVS. my architecture is x86-64, and compiler
is gcc.  thanks.
I will try 3.3.3
-Xianghong Qi

On Tue, Sep 16, 2008 at 4:02 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:

>
>
> xianghong qi wrote:
>
>> Hi, everyone:
>>
>> I am a beginner for Gromacs. I am using the latest version  Gromacs 4.0
>> beta1. Then I follow the tutorial part: Introduction to MD <
>> http://md.chem.rug.nl/education/mdcourse/> by the Groningen group.
>> Compiling is ok, but I always get the Segmentation fault when I use command
>> : genbox -cp minimized_box.gro -cs spc216.gro -o minimized_water.gro -p
>> aki.top. Also I get the same problem when i try other exercises.  Does
>> anyone has same problem like me ? or can anyone
>> give me a hint for that?  Thanks in advance.
>>
>
> It sounds like your installation is faulty.  What architecture are you
> running on?  What compilers did you use?
>
> If you are just starting out, it is probably better to use an official
> release of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in
> development.
>
> -Justin
>
>
>> -Xianghong Qi
>>
>> --
>> Postdoctoral Associate
>> Department of Chemistry
>> University of Pittsburgh
>> Chevron Science Center
>> 219 Parkman Avenue
>> Pittsburgh, PA 15260
>> Office: 338 EBERLY
>> Phone: 412-383-5400
>>
>>
>> Some people make the world more special just by being in it.
>>
>>
>> 
>>
>> ___
>> gmx-users mailing listgmx-users@gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
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>>
>
> --
> 
>
> Justin A. Lemkul
> Graduate Research Assistant
> 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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>



-- 
Postdoctoral Associate
Department of Chemistry
University of Pittsburgh
Chevron Science Center
219 Parkman Avenue
Pittsburgh, PA 15260
Office: 338 EBERLY
Phone: 412-383-5400


Some people make the world more special just by being in it.
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Re: [gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1

2008-09-16 Thread Justin A. Lemkul 



xianghong qi wrote:

Hi, everyone:

I am a beginner for Gromacs. I am using the latest version  Gromacs 4.0 
beta1. Then I follow the tutorial part: Introduction to MD 
 by the Groningen group. 
Compiling is ok, but I always get the Segmentation fault when I use 
command : genbox -cp minimized_box.gro -cs spc216.gro -o 
minimized_water.gro -p aki.top. Also I get the same problem when i try 
other exercises.  Does anyone has same problem like me ? or can anyone
give me a hint for that?  Thanks in advance. 


It sounds like your installation is faulty.  What architecture are you running 
on?  What compilers did you use?


If you are just starting out, it is probably better to use an official release 
of Gromacs (the latest being 3.3.3), since 4.0beta1 is still in development.


-Justin



-Xianghong Qi

--
Postdoctoral Associate
Department of Chemistry
University of Pittsburgh
Chevron Science Center
219 Parkman Avenue
Pittsburgh, PA 15260
Office: 338 EBERLY
Phone: 412-383-5400


Some people make the world more special just by being in it.




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--


Justin A. Lemkul
Graduate Research Assistant
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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[gmx-users] Re: Segmentation fault in Gromacs 4.0 beta1

2008-09-16 Thread xianghong qi 
Hi, everyone:

I am a beginner for Gromacs. I am using the latest version  Gromacs 4.0
beta1. Then I follow the tutorial part: Introduction to
MDby the Groningen group.
Compiling is ok, but I always get the Segmentation
fault when I use command : genbox -cp minimized_box.gro -cs spc216.gro -o
minimized_water.gro -p aki.top. Also I get the same problem when i try other
exercises.  Does anyone has same problem like me ? or can anyone
give me a hint for that?  Thanks in advance.

-Xianghong Qi

-- 
Postdoctoral Associate
Department of Chemistry
University of Pittsburgh
Chevron Science Center
219 Parkman Avenue
Pittsburgh, PA 15260
Office: 338 EBERLY
Phone: 412-383-5400


Some people make the world more special just by being in it.
___
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