[gmx-users] Xenon non-bonded parameterization

[Morgan Lawrenz]

>
>> Hi all, I am doing umbrella sampling on 2 Xenon atoms in a  
>> solvated 3 nm
>> box, with the atoms were parameterized according to
>
>> Dietmar Paschek, et al. (2004) Temperature dependence of the  
>> hydrophobic hydration and interaction of simple solutes: An  
>> examination of five popular water models. The Journal of Chemical  
>> Physics. 20, 6674-6690.
>> http://scitation.aip.org/getabs/servlet/GetabsServlet? 
>> prog=normal&id=JCPSA6000120000014006674000001&idtype=cvips&gifs=yes
>
>> Using GROMACS, I applied an umbrella potential to the two atoms  
>> moved along a distance of 10 Å with a force constant k = 5000 kJ  
>> mol−1 nm−2 for 2 ps time steps for 1500000 steps, total  
>> simulation time 3 ns.
>> My resulting PMF has a first minima around 2.5 angstroms, which is  
>> at too short a distance to be correct... I feel like some  
>> repulsive parameter is either incorrect or left out, but for all  
>> my troubleshooting, I cannot find out what it is. Any suggestions  
>> would be greatly appreciated, I am providing my topology  
>> information below:
>
>> Xe.itp
>> ;name    at. no.   mass      charge ptype  c6           c12
>>    Xe    54        131.293   0.000  A      2.815e-02  1.110e-04
>> #Xenon LJ parameters from sigma = 0.3975 nm and epsilon =  
>> 2.9643*10^-24 KJ
>>
>> [ nonbond_params ]
>>   ; i    j    func    c6          c12
>>    Xe    Xe     1     2.815e-02   1.110e-04
>>    Xe    OW     1     8.591e-03   1.71045e-05
>>    Xe    H      1     1.992e-03   2.775e-06
>> #Used OW parameters from gromacs library, found hydrogen values  
>> online, but gromacs has the H LJ set to zero - wondering if this  
>> is a problem?
>> XEN.itp
>> [ moleculetype ]
>>
>> ;   name  nrexcl
>>   XEN       3
>>
>> [ atoms ]
>> ;     id   atype   resnr resname   aname    cgnr  charge    mass
>>        1     Xe       1   XEN      Xe       0             
>> 0.0000      131.293
>>
>> System.top
>> #include "ffgmx.itp"
>>
>> ; Include topologies
>> #include "Xe.itp"
>> #include "XEN.itp"
>> #include "spce.itp"
>>
>>
>> [ system ]
>> ; Xenon
>>
>> [ molecules ]
>> ; Compound        #mols
>> XEN              2
>> SOL               892
>
>
>

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