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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--
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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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