<HTML><BODY style="word-wrap: break-word; -khtml-nbsp-mode: space; -khtml-line-break: after-white-space; "><DIV><DIV><BR class="khtml-block-placeholder"></DIV><BLOCKQUOTE type="cite"><DIV><BR class="Apple-interchange-newline"><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hi all, I am doing umbrella sampling on 2 Xenon atoms in a solvated 3 nm</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">box, with the <SPAN style="">atoms were parameterized according to </SPAN></DIV></BLOCKQUOTE><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN style=""><SPAN style="">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.</SPAN><SPAN style=""> 20, 6674-6690.</SPAN></SPAN><SPAN style=""><BR></SPAN></DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><A href="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</A></DIV></BLOCKQUOTE><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN style="">Using GROMACS, I applied an umbrella potential to the two atoms moved along a distance of 10 Å with a force constant k</SPAN><SPAN style=""> = 5000 kJ mol−1 nm−2</SPAN><SPAN style=""> </SPAN><SPAN style="">for 2 ps time steps for 1500000 steps, total simulation time 3 ns.</SPAN> </DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">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: </DIV></BLOCKQUOTE><BR><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><B>Xe.itp</B></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">;name<SPAN class="Apple-converted-space"> </SPAN>at. no. <SPAN class="Apple-converted-space"> </SPAN>mass<SPAN class="Apple-converted-space"> </SPAN>charge ptype<SPAN class="Apple-converted-space"> </SPAN>c6 <SPAN class="Apple-converted-space"> </SPAN>c12</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Xe<SPAN class="Apple-converted-space"> </SPAN>54<SPAN class="Apple-converted-space"> </SPAN>131.293 <SPAN class="Apple-converted-space"> </SPAN>0.000<SPAN class="Apple-converted-space"> </SPAN>A<SPAN class="Apple-converted-space"> </SPAN>2.815e-02<SPAN class="Apple-converted-space"> </SPAN>1.110e-04</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">#Xenon LJ parameters from sigma = 0.3975 nm and epsilon = 2.9643*10^-24 KJ</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">[ nonbond_params ]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>; i<SPAN class="Apple-converted-space"> </SPAN>j<SPAN class="Apple-converted-space"> </SPAN>func<SPAN class="Apple-converted-space"> </SPAN>c6<SPAN class="Apple-converted-space"> </SPAN>c12</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Xe<SPAN class="Apple-converted-space"> </SPAN>Xe <SPAN class="Apple-converted-space"> </SPAN>1 <SPAN class="Apple-converted-space"> </SPAN>2.815e-02 <SPAN class="Apple-converted-space"> </SPAN>1.110e-04</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Xe<SPAN class="Apple-converted-space"> </SPAN>OW <SPAN class="Apple-converted-space"> </SPAN>1 <SPAN class="Apple-converted-space"> </SPAN>8.591e-03 <SPAN class="Apple-converted-space"> </SPAN>1.71045e-05</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>Xe<SPAN class="Apple-converted-space"> </SPAN>H<SPAN class="Apple-converted-space"> </SPAN>1 <SPAN class="Apple-converted-space"> </SPAN>1.992e-03 <SPAN class="Apple-converted-space"> </SPAN>2.775e-06</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; ">#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?</DIV></BLOCKQUOTE><BLOCKQUOTE type="cite"><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><B>XEN.itp</B></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">[ moleculetype ]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">; <SPAN class="Apple-converted-space"> </SPAN>name<SPAN class="Apple-converted-space"> </SPAN>nrexcl</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>XEN <SPAN class="Apple-converted-space"> </SPAN>3</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">[ atoms ]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">; <SPAN class="Apple-converted-space"> </SPAN>id <SPAN class="Apple-converted-space"> </SPAN>atype <SPAN class="Apple-converted-space"> </SPAN>resnr resname <SPAN class="Apple-converted-space"> </SPAN>aname<SPAN class="Apple-converted-space"> </SPAN>cgnr<SPAN class="Apple-converted-space"> </SPAN>charge<SPAN class="Apple-converted-space"> </SPAN>mass</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><SPAN class="Apple-converted-space"> </SPAN>1 <SPAN class="Apple-converted-space"> </SPAN>Xe <SPAN class="Apple-converted-space"> </SPAN>1 <SPAN class="Apple-converted-space"> </SPAN>XEN<SPAN class="Apple-converted-space"> </SPAN>Xe <SPAN class="Apple-converted-space"> </SPAN>0<SPAN class="Apple-converted-space"> </SPAN>0.0000<SPAN class="Apple-converted-space"> </SPAN>131.293</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><B>System.top</B></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">#include "ffgmx.itp"</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">; Include topologies</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">#include "Xe.itp"</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">#include "XEN.itp"</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">#include "spce.itp"</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">[ system ]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">; Xenon</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; min-height: 14px; "><BR></DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">[ molecules ]</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">; Compound<SPAN class="Apple-converted-space"> </SPAN>#mols</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">XEN<SPAN class="Apple-converted-space"> </SPAN>2</DIV><DIV style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">SOL <SPAN class="Apple-converted-space"> </SPAN>892</DIV></BLOCKQUOTE><BR></DIV><DIV><BR class="khtml-block-placeholder"></DIV><BR></BLOCKQUOTE></DIV><BR></BODY></HTML>