<html><head><style type="text/css"><!-- DIV {margin:0px;} --></style></head><body><div style="font-family:'times new roman', 'new york', times, serif;font-size:12pt"><div>Thanks. The molecule was developed as a part of OPLS. The authors used a software called BOSS( developed in Bill Jorgensen's lab) . I guess this softwares have way to perform rigid body motion. There are other softwares like DL-POLY which can perform rigid body MD. So, I guess, in those cases, just declaring a molecule 'rigid' might be good enough. </div><div>But, gromacs does not explicitly do rigid body MD. That's why I was looking for a trick .</div><div><br></div><div style="font-family:times new roman, new york, times, serif;font-size:12pt"><br><div style="font-family:arial, helvetica, sans-serif;font-size:13px"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Justin A. Lemkul <jalemkul@vt.edu><br><b><span style="font-weight:
bold;">To:</span></b> Discussion list for GROMACS users <gmx-users@gromacs.org><br><b><span style="font-weight: bold;">Sent:</span></b> Wed, April 27, 2011 8:25:05 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] rigid tetrahedral molecule<br></font><br>
<br><br>Sanku M wrote:<br>> Hi,<br>> I am interested in simulating a anionic molecule BF4(-) ( Boron tetrafluoride). In the paper which developed the parameters for this molecule, it is mentioned that it has been used as 'rigid' molecule i.e the molecule only has non-bonding interaction but there was no intramolecular motion as the geometry was fixed.<br>> I am trying to simulate this molecule in gromacs treating it as rigid. But, I was looking for best way to 'rigidify' this molecule.<br>> <br>> I was wondering whether using LINCS to constrain all B-F and F-F bonds will be good enough . Or, Should I use virtual sites ? If I really need to use virtual site, will it be something like TIP5P water model ?<br>> Can someone suggest the best wayout ?<br>> <br><br>Constraints should do the trick, but probably the best approach is to simply contact the authors who developed the model and ask how
they did it. Then you know you're exactly reproducing what they did.<br><br>-Justin<br><br>> Sanku<br>> <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 target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><span><a target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a></span><br><br>========================================<br>-- gmx-users mailing list <a ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><span><a target="_blank"
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