<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><br></div><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><br><div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight: bold;">From:</span></b> Adrien Delmont <adriendelmont@yahoo.com><br><b><span style="font-weight: bold;">To:</span></b> jalemkul@vt.edu<br><b><span style="font-weight: bold;">Sent:</span></b> Wednesday, March 11, 2009 6:09:53 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] get a box of 100 molecules<br></font><br>
<div style="font-family: times new roman,new york,times,serif; font-size: 12pt;"><div>I didn't get gro and top files with any force field in Gromacs. I basicly want to use oplsaa and GROMOS96 43a2 force field (improved alkane dihedrals) . I think I should add all the parameters but how can I add my parametes both into oplsaa and GROMOS96 43a2 force field ?<br><br>Thanks in advance<br><br><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> Wednesday, March
11, 2009 5:48:59 PM<br><b><span style="font-weight: bold;">Subject:</span></b> Re: [gmx-users] get a box of 100 molecules<br></font><br>
<br><br>Adrien Delmont wrote:<br>> /Dear Users,<br>> <br>> I'm new to Gromacs. Before I try to generate a box of 100 molecules, I wanted to ask it to the users. Can I get a box of 100 molecules that are randomly //distributed/ /and not attached to each other using the commands below? If there are something wrong in commands please share your valuable suggestions with me. <br><br>Try it and see.<br><br>> Thanks in advance<br>> ///<br>> Adrien<br>> <br>> pdb2gmx -f mol.pdb -o mol.gro -p mol.top -i mol.itp ( then chose suitable force field )<br>> ////<br><br>This will only work if the force field contains parameters for your molecule.<br><br>-Justin<br><br>> //////////genbox////////// //////////-ci////////// mol.gro //////////-nmol 100//////// //-o 100mol.gro //////-p<br>> 100mol.top//// ////////-box 12 12 12//////////<br>> <br>> //<br>> <br>> <br>> <br>>
------------------------------------------------------------------------<br>> <br>> _______________________________________________<br>> gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>> <a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>> Please search the archive at <a rel="nofollow" target="_blank" href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>> Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>> Can't post? Read <a rel="nofollow" target="_blank"
href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br><br>--
========================================<br><br>Justin A. Lemkul<br>Graduate Research Assistant<br>ICTAS Doctoral Scholar<br>Department of Biochemistry<br>Virginia Tech<br>Blacksburg, VA<br>jalemkul[at]<a rel="nofollow" target="_blank" href="http://vt.edu">vt.edu</a> | (540) 231-9080<br><a rel="nofollow" target="_blank" href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br><br>========================================<br>_______________________________________________<br>gmx-users mailing list <a rel="nofollow" ymailto="mailto:gmx-users@gromacs.org" target="_blank" href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailman/listinfo/gmx-users">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>Please search the archive at <a rel="nofollow" target="_blank"
href="http://www.gromacs.org/search">http://www.gromacs.org/search</a> before posting!<br>Please don't post (un)subscribe
requests to the list. Use the www interface or send it to <a rel="nofollow" ymailto="mailto:gmx-users-request@gromacs.org" target="_blank" href="mailto:gmx-users-request@gromacs.org">gmx-users-request@gromacs.org</a>.<br>Can't post? Read <a rel="nofollow" target="_blank" href="http://www.gromacs.org/mailing_lists/users.php">http://www.gromacs.org/mailing_lists/users.php</a><br></div></div></div><br>
</div></div></div><br>
</body></html>