[gmx-users] Xenon non-bonded parameterization

[David van der Spoel]

Arneh Babakhani wrote:
> 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

yes

try it in vacuum first.
> 
> 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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>>>
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>>
>>
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se