[gmx-users] velacc & box of water

Justin A. Lemkul jalemkul at vt.edu
Sun Oct 11 02:39:35 CEST 2009

Jamie Seyed wrote:
> Dear Gmx Users,
> I have a 2 questions. First about g_velacc and calculating the diffusion 
> constant from that. In mailing list people say that we need to divide it 
> by mass squared and 1/3. Then I found another recent post that said it 
> has been included in the code... Would you please clarify this that if I 
> need the factors or not. Also I found 2 numbers after integration.
> Integral   1   0.01595
> set    average
> SS1   3.718082e-04
> --1) Would you please inform me what are these number and what is the 
> relation between them?

Can't comment on the first part...maybe the code will point you in the right 

> --2) My second question is I want to make a box of only water (spce) 
> with let say 500 water molecules. Would you please give me quick hints 
> how to do it (the proper way) or refer me to good point? Up to now I can 
> only have 216 water molecules from tuto/water folder and I tried a lot 

This task might be approached in a couple of ways:

1. genconf -nbox to define a suitable number of replicate systems.
2. genbox -box -maxsol 500 to define a suitably-sized box and fill it with only 
the desired number of molecules.


> to start from the beginning, but I could not make it... I appreciate if 
> you help me to understand the first issue and be able to overcome the 
> second one. Many Thanks in Advance/Jamie
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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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