[gmx-users] g_sas by 3.3.1 and 3.3.2 give different results

[Yin Jian]

Thank you very much David.
Great. The installment is done. My PC screen was busy on showing 
alot of lines which I do not really know almost a single one.

Have a good day


Regards,
Jian Yin

-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of David van der Spoel
Sent: Friday, October 12, 2007 1:09 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] g_sas by 3.3.1 and 3.3.2 give different results

Yin Jian wrote:
> 
> Hi Mark,
> Since I have only a user account, I cannot install the version 3.3.2 
> by myself into our system.  The command I used are:
> g_sas -f 1hz3_model01_cg_genbox_md2.xtc -s 
> 1hz3_model01_cg_genbox_md2.tpr -n 1hz3_model01_cg_genbox.ndx -o 
> md2.abeta_sas and ~/bin/g_sas -f 1hz3_model01_cg_genbox_md2.xtc -s 
> 1hz3_model01_cg_genbox_md2.tpr -n 1hz3_model01_cg_genbox.ndx -o 
> md2.abeta_sas for module g_sas in version 3.3.1 and 3.3.2, 
> respectively.
> 
> Could you please tell me if I could install a local version of 3.3.2 
> instead of this dirty trick, I would appreciate it.

 From source it is easy, just use the ./configure
--prefix=/home/jian/gromacs332

For your g_sas problem, please submit a bugzilla. I could have
introduced a problem there.
> 
> 
> Thanks for your reply.
> 
> 
> Regards,
> Jian Yin
> 
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org
> [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Mark Abraham
> Sent: Friday, October 12, 2007 10:59 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] g_sas by 3.3.1 and 3.3.2 give different 
> results
> 
> Yin Jian wrote:
>> Hi David,
>> I used g_sas modules in version 3.3.1 and 3.3.2 but got not the Same 
>> results as follows ================================ tail sas331.xvg 
>> sas332.xvg ==> sas331.xvg <==
>>     399982     20.4122     3.54058     23.9528     25.8919
>>     399984     20.3506     3.38663     23.7372     27.7211
>>     399986     19.9196     3.60215     23.5217     25.9177
>>     399988     19.6425     3.54057     23.1831     26.6648
>>     399990     20.3814     3.41742     23.7988     25.7631
>>     399992     20.2582     3.35585     23.6141     25.9176
>>     399994     20.5661     3.38664     23.9528     26.8451
>>     399996     19.1807       3.479     22.6597     25.5827
>>     399998     19.7656     3.38663     23.1523     25.0932
>>     400000     20.8432     3.41742     24.2606      26.639
>>
>> ==> sas332.xvg <==
>>     399982     20.9664      2.9864     23.9528    -1.15934
>>     399984     22.3826     1.35466     23.7372     4.01904
>>     399986     21.5205     2.00119     23.5217   -0.721367
>>     399988     21.1511     2.03198     23.1831     4.86922
>>     399990     20.8124     2.98639     23.7988    -7.65164
>>     399992     20.8124     2.80167     23.6141     9.42928
>>     399994      22.321     1.63174     23.9528     6.23466
>>     399996     20.7201     1.93962     22.6597     10.6917
>>     399998     20.6277     2.52458     23.1523    -4.94651
>>     400000      22.752     1.50859     24.2606     3.73564
>> =====================================
>> What's the matter? Thanks
> 
> Please provide your command lines, system description, etc. The above 
> is like telling your car mechanic that your old car doesn't do the 
> same thing as your new car. He'll shrug and do nothing until you give 
> him something useful to work with.
> 
> Mark
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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