<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>Hi David,</div><div> Actually, I had tried to use vsites to make this molecule rigid. I read the manual section 4.7 as well. But, unfortunately, for a 5-site tetrahedral geometry I was not able to figure out the right vsite type I should use. So, I was wondering whether you can provide some input on the details of how to use virtual sites for a tetrahedral molecule. It would have been helpful.</div><div>Sanku</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> David van der Spoel <spoel@xray.bmc.uu.se><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> Fri, April 29, 2011 11:46:01 AM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] rigid tetrahedral molecule<br></font><br>
On 2011-04-29 17.55, <a ymailto="mailto:gyorgy.hantal@fc.up.pt" href="mailto:gyorgy.hantal@fc.up.pt">gyorgy.hantal@fc.up.pt</a> wrote:<br>><br>> Hi Sanku,<br>><br>> I've read about your problem just now, I don't know if it's already<br>> solved but I had the same problem some weeks ago and I also had a lot of<br>> troubles. But, finally I managed to solve it so maybe my experiences can<br>> be helpful for you:<br>><br>> I think you should use SHAKE instead of LINCS. The manual says somewhere<br>> that LINCS cannot be used when constraining triangles (i.e. angles) but<br>> SHAKE works fine. On the other hand, if you use SHAKE you must switch<br>> from domain decomposition to particle decomposition (if you run your<br>> simulations parallel) just by using -pd when you type mdrun ('domain<br>> decomposition = no' in the mdp file is not enough).<br>><br>> Then you must add as many constraints as degrees of
freedom you have, so<br>> 9 in your case. In my case it was 15 for the PF6 anion. Maybe it'll work<br>> with less than 9 but in my case I had to add 15 contraints. What I did<br>> was the following:<br>> First I constrained all P-F bonds then I constrained fictious F-F bonds<br>> that I thought would make the molecule rigid. But it wasn't enough. Then<br>> I added some more redundant F-F contraints (up to 15 in total) in a bit<br>> arbitrary way until I found the 'magic combination'.<br>> Now my simulations run perfectly.<br>><br>Please note that if your rigid molecule has less than 6 degrees of <br>freedom your temperature will be incorrect!<br>You can achieve a solution with the right number of d.o.f. by using <br>vsites as well. How to do this is left as an exercise for the reader.<br><br>> I hope this helps.<br>><br>> best,<br>> Gyorgy<br>><br>><br>> Citando Sanku M <<a
ymailto="mailto:msanku65@yahoo.com" href="mailto:msanku65@yahoo.com">msanku65@yahoo.com</a>>:<br>><br>>> Thanks. The molecule was developed as a part of OPLS. The authors used a<br>>> software called BOSS( developed in Bill Jorgensen's lab) . I guess this<br>>> softwares have way to perform rigid body motion. There are other<br>>> softwares like<br>>> DL-POLY which can perform rigid body MD. So, I guess, in those cases,<br>>> just<br>>> declaring a molecule 'rigid' might be good enough.<br>>> But, gromacs does not explicitly do rigid body MD. That's why I was<br>>> looking for<br>>> a trick .<br>>><br>>><br>>><br>>><br>>> ________________________________<br>>> From: Justin A. Lemkul <<a ymailto="mailto:jalemkul@vt.edu" href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>><br>>> To: Discussion list for GROMACS users <<a
ymailto="mailto:gmx-users@gromacs.org" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>><br>>> Sent: Wed, April 27, 2011 8:25:05 PM<br>>> Subject: Re: [gmx-users] rigid tetrahedral molecule<br>>><br>>><br>>><br>>> Sanku M wrote:<br>>>> Hi,<br>>>> I am interested in simulating a anionic molecule BF4(-) ( Boron<br>>>> tetrafluoride). In the paper which developed the parameters for this<br>>>> molecule,<br>>>> it is mentioned that it has been used as 'rigid' molecule i.e the<br>>>> molecule only<br>>>> has non-bonding interaction but there was no intramolecular motion as<br>>>> the<br>>>> geometry was fixed.<br>>>> I am trying to simulate this molecule in gromacs treating it as<br>>>> rigid. But, I<br>>>> 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<br>>>> bonds will be<br>>>> good enough . Or, Should I use virtual sites ? If I really need to<br>>>> use virtual<br>>>> 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<br>>> simply<br>>> contact the authors who developed the model and ask how they did it.<br>>> Then you<br>>> 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" href="http://lists.gromacs.org/mailman/listinfo/gmx-users">http://lists.gromacs.org/mailman/listinfo/gmx-users</a></span><br>>> Please search the archive at<br><span>>> <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists/Search">http://www.gromacs.org/Support/Mailing_Lists/Search</a></span><br>>> before posting!<br>>> Please don't post (un)subscribe requests to the list. Use the
www<br>>> interface or<br>>> send it to <a ymailto="mailto:gmx-users-request@gromacs.org" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br><span>>> Can't post? Read <a target="_blank" href="http://www.gromacs.org/Support/Mailing_Lists">http://www.gromacs.org/Support/Mailing_Lists</a></span><br>>><br>><br>><br>><br><br><br>-- <br>David van der Spoel, Ph.D., Professor of Biology<br>Dept. of Cell & Molec. Biol., Uppsala University.<br>Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.<br><a ymailto="mailto:spoel@xray.bmc.uu.se" href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a><span> <a target="_blank" href="http://folding.bmc.uu.se">http://folding.bmc.uu.se</a></span><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><a
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