[gmx-users] VDWradii.dat

Justin A. Lemkul jalemkul at vt.edu
Mon Aug 30 21:17:37 CEST 2010

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;
         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).


> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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