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
direction?
--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.
-Justin
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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