[gmx-users] reg box dimension

Justin A. Lemkul jalemkul at vt.edu
Tue Sep 20 17:32:01 CEST 2011

vidhya sankar wrote:
> Dear justin,
>                    Thank you fro your previous reply
> when i run SMD using the same force ( same rate constant and same rate)  
> in different box having different dimension. will it affect the result  
> of simulation
> I am asking the effect of box dimension on pull in group (keeping 
> constant rate and rate constant)
> I am expecting your valuable reply
> Thanks in ADVANCE

Possibly, but your question is too vague to give any real advice.  Are you 
adjusting all box vectors, or just along the pulling dimension(s)?  How far are 
you pulling?  Does the pulled distance always remain less than 1/2 the box 
vector along the pulled dimension(s)?  Or are you using the direction_periodic 
geometry to circumvent this effect?



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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