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Thank you very much for the suggestion.<br> Actually, I am trying to
reproduce the results from another publication (JACS 2005, 127, 7166)
http://pubs.acs.org/doi/full/10.1021/ja050044d where they used
Gromacs/amber to simulate a CNT.<font style="font-size: 10pt;" size="2"><font style="" face="Times New Roman"> They apply: </font></font>"Carbon−carbon bond lengths of 0.14 nm and bond angles of 120° were
maintained by harmonic potentials with spring constants of 393 960 kJ
mol<sup>-</sup><sup>1</sup> nm<sup>-</sup><sup>2</sup> and 527 kJ mol<sup>-</sup><sup>1</sup> deg<sup>-</sup><sup>2</sup> before relaxation. In addition, a weak dihedral angle potential was applied to bonded carbon atoms.<sup>" <br><br></sup>So, as I understand, they apply RESTRAINTS to the bonds, angles and dihedrals.<br><br>I have tried to construct the [distance_restraints] for my system (I show you here a little part):<br><br>[ distance_restraints ]<br>; atom1 atom2 type index type2 low up1 up2 fac<br>1 310 1 1 1 0.142 0.146 0.150 1.0<br>2 290 1 2 1 0.142 0.146 0.150 1.0<br>3 291 1 3 1 0.142 0.146 0.150 1.0<br>(...)<br><br>but
I don' t understand very well which value should I write for "low
up1 up2". The manual says that "the columns low, up1 and up2 hold the
values of r0 , r1 and r2 from eqn. 4.76", but looking at this equation
I still don' t understand which should be the better values for my
case. I have looked into the mail archive, and some other people asked
for that, but I did not find any proper solution.<br>How could I choose the best values for "low up1 up2" to restrain my bond values to 1.42 Amstrong?<br><br>The
other question is about angle restraints, I have found indications in
the wiki of how to treat the dihedral restraints
(http://wiki.gromacs.org/index.php/Dihedral_Restraints), however I did
not find any similar for the angle restraints. I have seen in the mail
archive that 2 pairs of atoms should be used, but I did not find
anything to trust in. Could you please give me some indications of how
to treat angle restraints?<br><br>Thank you very much,<br><br>Best wishes, <br><br>Rebeca Garcia<br>Parc Cientific de Barcelona<br>Spain<br><br>> Date: Thu, 21 May 2009 12:41:57 -0400<br>> From: jalemkul@vt.edu<br>> To: gmx-users@gromacs.org<br>> Subject: Re: [gmx-users] bond, angle and dihedral restraints in Gromacs<br>> <br>> <br>> <br>> Rebeca García Fandiño wrote:<br>> > Hello,<br>> > I would like to simulate a CNT and I want to apply a harmonic potential:<br>> > -on the C-C bonds<br>> > -on the bond angles<br>> > -on the dihedral angles<br>> > with a different spring constant for each case.<br>> > <br>> > I have read Section 4.3 from Gromacs manual, but I actually have some <br>> > doubts about how to include this in the topology.<br>> > <br>> > -for the distance restraints I have tried to use genrestr:<br>> > <br>> > genrestr -f cnt_wat_gmx_centered.gro -o posre_dist.itp -disre -fc 400000<br>> > <br>> > The file I obtain is something like:<br>> > <br>> > ; distance restraints for UNK of cnt_wat_gmx.gro created by <br>> > rdparm2gmx.pl Wed May 20 10:20:59 BST 2009<br>> > <br>> > [ distance_restraints ]<br>> > ; i j ? label funct lo up1 up2 weight<br>> > 1 2 1 0 1 0.403354 0.603354 1.60335 1<br>> > 1 3 1 1 1 0.587676 0.787676 1.78768 1<br>> > 1 4 1 2 1 0.769212 0.969212 1.96921 1<br>> > 1 5 1 3 1 0.86081 1.06081 2.06081 1<br>> > (...)<br>> > <br>> > This is different from the [distance_restraint] example shown in pag 69 <br>> > of the manual, now I don' t have the fac column. I would like to apply a<br>> <br>> The format of the distance_restraints section appears correct. If you read the <br>> description of the "fac" column, it is a weighting factor for that particular <br>> restraint. So therefore, "weight" is probably equivalent.<br>> <br>> > spring constant of 400000 to C-C bonds, but where is the constant here? <br>> > How could I apply a determined spring constant? In the .mdp file? <br>> > Besides, all the distances are restrained... Is there any way to <br>> > restrain only the C-C bonds? I mean I don' t want to restrain the <br>> > distance between a carbon and a carbon far away from it, only <br>> > restraining the neighbouring carbons to a distance of 1.4 A.<br>> > <br>> <br>> You cannot use genrestr for this purpose. Using genrestr -disre generates a <br>> matrix of all atoms you specify. Also, -fc is expected to be used with position <br>> restraints; note the format given in genrestr -h.<br>> <br>> Are you really interested in applying restraints to all bonds, angles, <br>> dihedrals, and distances? Realize that constraints (Section 5.5) and restraints <br>> are separate ideas in Gromacs.<br>> <br>> If you want to define your own force constants for bonds, angles, etc. simply do <br>> so in the topology yourself (Table 5.4).<br>> <br>> -Justin<br>> <br>> > Another question is: Is there any tool to construct the equivalent <br>> > angle_restraints and dihedral_restraints in an authomatic way, or should <br>> > I do it by hand?<br>> > <br>> > Thank you very much in advance for your help.<br>> > <br>> > Best wishes,<br>> > <br>> > Dr. Rebeca Garcia<br>> > Parc Cientific de Barcelona<br>> > Spain<br>> > <br>> > <br>> > <br>> > <br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > Haz búsquedas con Live Search, ¡todas tus búsquedas tienen premio! <br>> > <http://www.buscalasuerte.com/><br>> > <br>> > <br>> > ------------------------------------------------------------------------<br>> > <br>> > _______________________________________________<br>> > gmx-users mailing list gmx-users@gromacs.org<br>> > http://www.gromacs.org/mailman/listinfo/gmx-users<br>> > Please search the archive at http://www.gromacs.org/search before posting!<br>> > Please don't post (un)subscribe requests to the list. Use the <br>> > www interface or send it to gmx-users-request@gromacs.org.<br>> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br>> <br>> -- <br>> ========================================<br>> <br>> Justin A. Lemkul<br>> Ph.D. Candidate<br>> ICTAS Doctoral Scholar<br>> Department of Biochemistry<br>> Virginia Tech<br>> Blacksburg, VA<br>> jalemkul[at]vt.edu | (540) 231-9080<br>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin<br>> <br>> ========================================<br>> _______________________________________________<br>> gmx-users mailing list gmx-users@gromacs.org<br>> http://www.gromacs.org/mailman/listinfo/gmx-users<br>> Please search the archive at http://www.gromacs.org/search before posting!<br>> Please don't post (un)subscribe requests to the list. Use the <br>> www interface or send it to gmx-users-request@gromacs.org.<br>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php<br><br /><hr />¿Eres del Madrid, del Barça, del Atleti...? Apoya a tu equipo en la <a href='http://opiniones.msn.es/default.aspx/Futbol/Atletico-de-Madrid ' target='_new'>Zona Fan de MSN Deportes</a></body>
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