[gmx-users] velacc & box of water

Jamie Seyed jamie.seyed at gmail.com
Sun Oct 11 02:21:38 CEST 2009

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?

--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 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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