[gmx-users] Xenon non-bonded parameterization

[David van der Spoel]

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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-- 
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