[gmx-users] velacc & box of water

[Jamie Seyed]

Thanks to Justin & Mark for answering my second question...
Could any one give me a hint on my first question that I copy it again?
--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
Would you please inform me what are these number and what is the relation
between them?
Many Thanks in Advance/Jamie

On Sat, Oct 10, 2009 at 8:39 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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