[gmx-users] VDWradii.dat

[nishap.patel at utoronto.ca]

Okay I see what you mean. Thanks alot!

Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:

>
>
> nishap.patel at utoronto.ca wrote:
>> I did use this command:
>>
>> editconf -f md.tpr -mead na.pqr. If I understand it correctly for   
>> -sig56 option, I would use the min rvdw from my mdp and divide it   
>> by 2 and use that value in the command line?
>
> The value of rvdw is taken from the -rvdw flag, per the description in
> editconf -h and the source code.
>
> If you take the code block (line 608 in gmx_editconf.c):
>
>       if (bSig56)
>         sig6 = 2*c12/c6;
>       else
>         sig6 = c12/c6;
>       vdw   = 0.5*pow(sig6,1.0/6.0);
>
> You can easily calculate the radius value you obtained (after
> converting sigma/epsilon for the atom type to C6/C12).
>
> -Justin
>
>>
>> Quoting David van der Spoel <spoel at xray.bmc.uu.se>:
>>
>>> On 2010-08-30 20.32, nishap.patel at utoronto.ca wrote:
>>>> Hello,
>>>>
>>>> I have a question about how gromacs assigns VDW radii for ions. I
>>>> checked the vdwradii.dat file but it does not mention any ions, so where
>>>> do the parameters for ions come from? I got the .pqr file for sodium and
>>>> I got the atomic radii of 1.6652A, I am not sure where that value came
>>>> from.
>>>>
>>>> I would really appreciate some help!
>>>>
>>>> Thanks.
>>>>
>>>> -Nisha P
>>>>
>>> Did you get the pqr file from editconf? Then read editconf -h.
>>> Check the -sig56 option.
>>>
>>> -- 
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Dept. of Cell & Molec. Biol., Uppsala University.
>>> Box 596, 75124 Uppsala, Sweden. Phone:    +46184714205.
>>> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
>>> -- 
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>>
>>
>>
>>
>
> -- 
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> 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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