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?
--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
genconf will allow you to stack multiples of that 216 box. Or, use
editconf to adjust the size of a 216 box, and genbox to fill it to get a
number that suits your fancy. In either case you will need to
equilibrate before trying to measure velacc, just as with any other
observable.
Mark
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