Dear gmx users,<br><br>I have a basic query.<br>With respect to which structure are the rmsf values calculated per each atom?<br><br>is it w.r.t average structure of the protein or the reference structure that we provide using -s option?<br>
<br>I dont find any explanation of the output generated using g_rmsf. Please make this clear.<br><br><br>Thanks!!<br>Swapna<br><br><br><br><div class="gmail_quote">On Mon, Apr 7, 2008 at 5:06 AM, Maik Goette <<a href="mailto:mgoette@mpi-bpc.mpg.de">mgoette@mpi-bpc.mpg.de</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">QL,<br>
<br>
1. Yes. I'd use version a) because of, the less dummies, the better.<br>
2. Yes<br>
3. Of course, charges have to vanish for dummies, too. Keep the bonded terms. If not, your dummies will "diffuse" away.<br>
<br>
Yes, your assumption about dummies is right.<br>
<br>
Actually, I won't use this system for your first perturbation. Take something simpler.<br>
Second, as indicated by point 3, you will have to tackle a disappearing netto charge of -1 (depending on the pH of course). This usually is a problem.<br>
There were discussions of PME being problematic here.<br>
Morphing an ion to counter that charge difference is possible. However, I think this would lead to a very bad equilibrated system and no reasonable results.<br>
<br>
Regards<br>
<br>
Maik Goette, Dipl. Biol.<br>
Max Planck Institute for Biophysical Chemistry<br>
Theoretical & computational biophysics department<br>
Am Fassberg 11<br>
37077 Goettingen<br>
Germany<br>
Tel. : ++49 551 201 2310<br>
Fax : ++49 551 201 2302<br>
Email : mgoette[at]<a href="http://mpi-bpc.mpg.de" target="_blank">mpi-bpc.mpg.de</a><br>
mgoette2[at]<a href="http://gwdg.de" target="_blank">gwdg.de</a><br>
WWW : <a href="http://www.mpibpc.gwdg.de/groups/grubmueller/" target="_blank">http://www.mpibpc.gwdg.de/groups/grubmueller/</a><br>
<br>
<br>
friendli wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
Dear Gmx users,<br>
<br>
I am calculating the mutation free energy from amino acid Asp to Asn as a test job for my practice.<br>
I have some questions about setting up the topology file.<br>
<br>
1, from Asp to Asn mutation, the -CH2-COOH changes to -CH2-CO-NH2 or simply -OH to -NH2.<br>
In topology, O <-> N.<br>
What about the hydrogens, do I need one or two dummy(DUM) atoms?<br>
<br>
a), DUM <-> H ; H(of OH) <-> H(of NH2)<br>
b), DUM <-> H(of NH2); DUM <-> H(of NH2); H(of OH) to DUM<br>
a) or b) should I use?<br>
<br>
2, I need to provide the coordinates for the dummy atoms in the .gro file(Asp), right? since otherwise the # of atoms in .top and .gro will mismatch.<br>
<br>
3, from the tutorial(methane) I read, the masses of the dummy atom keeps like real atom and the C6 and C12 changes to zero in [atomtypes] to vanish the nonbonded interactions. How to deal with the bonds and the charges for dummy atoms? bonded interactions?<br>
<br>
I think I am a bit confused by the definition of the dummy atom. I understanding is a dummy atom is a atoms with same mass but no interaction with all other atoms. Is that right?<br>
<br>
<br>
thanks for help and suggestions are appreciate.<br>
<br>
QL<br>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">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 href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
<br>
.<br>
<br>
</blockquote>
_______________________________________________<br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://www.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://www.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/search" target="_blank">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 href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/mailing_lists/users.php" target="_blank">http://www.gromacs.org/mailing_lists/users.php</a><br>
</blockquote></div><br><br clear="all"><br>-- <br>The logic of life lies exclusively neither in the most incredible detail, nor in the most sweeping synopsis.