[gmx-users] g_sas problem

[David van der Spoel]

tangxuan wrote:
> Hi Mark,
>  Thanks very much for your reply. I checked the structure of A and B at
> these three ps, and there is no much change in the structures. Then I
> calculated the reside area in A+B at these three specific time
> (1536,15937,15938), and it shows that there are a big diffrence in size
> of area at many resides between three ps. Maybe the big changes of total
> SAS in interaction region at 15938 ps is because of big size of two
> subunits(each has 471 resides). What is your idea?
> 
Tang, this is most likely all due to periodic boundary conditions. 
Please run
trjconv -pbc mol -ur compact on your trajectory.


> Thanks,
> 
> Tang jiaowei
> 
> On Wed, 2007-10-31 at 01:59 +1100, Mark Abraham wrote:
>> tangxuan wrote:
>>> Yes, the default value of -pbc is 'yes'. I did not add it in my command,
>>> but i think pbc should has been considered.  It seems there is no
>>> contact between the two subunits, but at some specific time the total
>>> ASA of interaction region is very high(shown below).
>>>
>>>   time     total SAS of interaction region 
>>>   15936   1.16099999999997
>>>   15937   1.09100000000004
>>>   15938   86.954
>> Have a look at your trajectory to see what the structures are doing here.
>>
>> Mark
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> 
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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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