[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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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