Hi, Justin, Thank you for your answer to my previous post. I just turned on the mail delivery from this list,<div>so I reply you here, hope it is not so disruptive to this thread.</div><div><br></div><div>My problem for the previous post is resolved, the problem is I should have modified files in ~username/gromacs/.., instead I modified </div>
<div>files in ~username/gromacs-4.0.7/... .</div><div><br></div><div>And regarding your advice:</div><div><span class="Apple-style-span" style="font-family: monospace, arial, sans-serif; font-size: medium; "><tt>"Some unsolicited advice: surely you want a negative charge on the fluorine, and </tt><tt>a bond between these two atoms, correct?</tt></span> "</div>
<div><br></div><div>I am using a HF dimer potential developed by Cournoyer and Jorgensen in 1984. Both H and F have a +0.725e charge, there is a virtue site which carries all the negative neutralizing</div><div>charges. My questions for you is : I don't need define the virtue site in .rtp file, right? And If I want the bond distance fixed, do I need put [ bond ] directive in the .rtp file? Is a </div>
<div>[ constraint ] in .itp file enough? </div><div><br></div><div>My intended application is using GROMACS to simulate a box of liquid HF.</div><div><br></div><div>Thank you!</div><div><br></div><div>Feng Xu (Postdoc@Iowa State University)<br>
<div><br><br><div class="gmail_quote">On Thu, Jan 7, 2010 at 2:11 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
On 1/7/10 2:58 PM, Hans HEINDL wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
interstingly the distance restrain works well when one chooses the bond<br>
type 2 whatever this means physically<br>
<br>
[bonds]<br>
<br>
.<br>
.<br>
.<br>
.<br>
.<br>
.<br>
1 614 2 5,761 400000<br>
</blockquote>
<br>
What you've specified is not a distance restraint, it is just a bond. Bond types are explained in the manual (Chapter 5), which should alleviate the "whatever this means" comment :)<br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br>
Hans<br>
<br>
</blockquote>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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