[gmx-users] Xenon non-bonded parameterization

[Arneh Babakhani]

Ok,

So since there are no LJ on H in SPC/E, 
should we eliminate the line the line:
Xe    H      1     1.992e-03   2.775e-06

to be more consistent???

David van der Spoel wrote:
> Morgan Lawrenz wrote:
>>
>>>
>>>> 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 
>>>> <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
>
> ./sigeps -c6 2.815e-02 -cn 1.110e-04
>
> c6    =  2.81500e-02, c12    =  1.11000e-04
> sigma =      0.39747, epsilon =      1.78474
> Van der Waals minimum at 0.446148, V = -1.78474
>
> You're right. How about combination rules? The parameters below are 
> not consistent with SPC/E which has no LJ on H.
>
>>>>
>>>> [ 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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>
>