<div>Hello!</div>
<div>Sorry to bother you again, but I have another question. I have written a topology file of two water molecules to test the pair interaction. Here is part of my topology file:</div>
<div> </div>
<div>[ moleculetype ]<br>SOL 2<br>[ atoms ]<br> 1 opls_116 1 SOL OW 1 -0.82<br> 2 opls_117 1 SOL HW1 1 0.41<br> 3 opls_117 1 SOL HW2 1 0.41<br> 4 opls_116 2 SOL OW 2 -0.82<br> 5 opls_117 2 SOL HW1 2 0.41<br>
6 opls_117 2 SOL HW2 2 0.41<br>[ settles ]<br> 1 1 0.1 0.16330<br> 4 1 0.1 0.16330<br>[ exclusions ]<br> 1 2 3<br> 2 1 3<br> 3 1 2<br> 4 5 6<br> 5 4 6<br> 6 4 5<br>[ exclusions ]<br>1 4</div>
<div>[ pairs ]<br> 1 4 1</div>
<div> </div>
<div>I have also changed the fudgeLJ and fudgeQQ to 1.0.</div>
<div>Originally, there is no pair interaction in this system. First I did a simulation when the last 4 lines were removed, that is, I treated all the interactions as non-bonded interactions. Then I added the last 4 lines to specify the normal non-bonded interaction between atom 1 and 4 as pair interaction in order to see whether that will affect the result. It turns out that the results for the two cases are different. So did I miss something, or are pair interactions and non-bonded interactions treated differently by GROMACS?<br>
Thanks in advance.<br><br></div>
<div class="gmail_quote">2009/7/28 Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span><br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">
<div class="im">Lee Soin wrote:<br>
<blockquote style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class="gmail_quote">So there is no place to specify electrostatic interactions for pair<br>interactions?<br></blockquote><br></div>
No. The charges are specified in the [ atoms ] directive. Read the example in chapter 5.
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<div class="h5"><br><br>Mark<br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
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<div></div><br>-- <br>SUN Li<br>Department of Physics<br>Nanjing University, China<br>