<div>Dear Mark and Gromacs Users,</div>
<div> </div>
<div>Can you be more specific in explanation about improper dihedral of charmm in gromacs?</div>
<div>For opls aa, it is very clear that every item of improper dihedral angle is described once</div>
<div>on the *rtp file.</div>
<div> </div>
<div>I am quite confused about the one in the charmm.</div>
<div>Ihe same angle is sometimes described twice despite of the difference in the atoms&#39; sequence.</div>
<div> </div>
<div>Suposed for an unkown molecule, how to assign them on rtp file?</div>
<div> </div>
<div>Can you give some introduction or show somewhere that has the document?</div>
<div>Gromacs menu does not document about this.</div>
<div> </div>
<div>Thanks for advance!</div>
<div> </div>
<div>Tom <br></div>
<div class="gmail_quote">
<blockquote style="BORDER-LEFT:#ccc 1px solid;MARGIN:0px 0px 0px 0.8ex;PADDING-LEFT:1ex" class="gmail_quote"><br>Message: 1<br>Date: Sat, 11 Feb 2012 11:15:04 +1100<br>From: Mark Abraham &lt;<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>&gt;<br>
Subject: Re: [gmx-users] improper dihedral angle in charmm and opls aa<br>To: Discussion list for GROMACS users &lt;<a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a>&gt;<br>Message-ID: &lt;<a href="mailto:4F35B308.3080504@anu.edu.au">4F35B308.3080504@anu.edu.au</a>&gt;<br>
Content-Type: text/plain; charset=&quot;iso-8859-1&quot;<br><br>On 11/02/2012 9:54 AM, Tom wrote:<br>&gt; Dear Gromacs Users<br>&gt; I am confused about definition of improper dihedral angle in charmm27,<br>&gt; which is compared to oplsaa.<br>
&gt; Why charmm ff in gromacs give *double* items for the same dihedral angle.<br>&gt; e.g.  for charmm27 ASN<br>&gt;         CG      ND2     CB      OD1<br>&gt; CG      CB      ND2     OD1<br>&gt;         ND2     CG      HD21    HD22<br>
&gt; ND2     CG      HD22    HD21<br><br>These are not duplicates. Atom ordering is significant. These *improper*<br>dihedral angles are enforcing planarity of the amide moiety. This is<br>done by influencing dihedral angles along intra-atom vectors where there<br>
is no bond. OPLS/AA is working differently somehow.<br><br>Mark<br><br>&gt; in opls aa for ASN<br>&gt;     CG    CB    CA     C     dih_ASN_chi1_C_C_C_CO<br>&gt;     CA    CB    CG   ND2     dih_ASN_chi2_C_C_CO_N<br>&gt; Thanks for advance!<br>
&gt; Tom<br>&gt; PS:<br>&gt; the detail is as follows<br>&gt; ------------------------------------------------<br>&gt; *in charmm27.ff/aminoacids.rtp*<br>&gt; [ ASN ]<br>&gt;  [ atoms ]<br>&gt;         N       NH1     -0.47   0<br>
&gt;         HN      H       0.31    1<br>&gt;         CA      CT1     0.07    2<br>&gt;         HA      HB      0.09    3<br>&gt;         CB      CT2     -0.18   4<br>&gt;         HB1     HA      0.09    5<br>&gt;         HB2     HA      0.09    6<br>
&gt;         CG      CC      0.55    7<br>&gt;         OD1     O       -0.55   8<br>&gt;         ND2     NH2     -0.62   9<br>&gt;         HD21    H       0.32    10<br>&gt;         HD22    H       0.30    11<br>&gt;         C       C       0.51    12<br>
&gt;         O       O       -0.51   13<br>&gt;  [ bonds ]<br>&gt;         CB      CA<br>&gt;         CG      CB<br>&gt;         ND2     CG<br>&gt;         N       HN<br>&gt;         N       CA<br>&gt;         C       CA<br>
&gt;         C       +N<br>&gt;         CA      HA<br>&gt;         CB      HB1<br>&gt;         CB      HB2<br>&gt;         ND2     HD21<br>&gt;         ND2     HD22<br>&gt;         C       O<br>&gt;         CG      OD1<br>
&gt;  [ impropers ]<br>&gt;         N       -C      CA      HN<br>&gt;         C       CA      +N      O<br>&gt;         CG      ND2     CB      OD1<br>&gt;         CG      CB      ND2     OD1<br>&gt;         ND2     CG      HD21    HD22<br>
&gt;         ND2     CG      HD22    HD21<br>&gt;  [ cmap ]<br>&gt;         -C      N       CA      C       +N<br>&gt; -------------------------------------------<br>&gt; in*oplsaa.ff/aminoacids.rtp*<br>&gt; [ ASN ]<br>&gt;  [ atoms ]<br>
&gt;      N    opls_238   -0.500     0<br>&gt;      H    opls_241    0.300     0<br>&gt;     CA    opls_224B   0.140     1<br>&gt;     HA    opls_140    0.060     1<br>&gt;     CB    opls_136   -0.120     2<br>&gt;    HB1    opls_140    0.060     2<br>
&gt;    HB2    opls_140    0.060     2<br>&gt;     CG    opls_235    0.500     3<br>&gt;    OD1    opls_236   -0.500     3<br>&gt;    ND2    opls_237   -0.760     4<br>&gt;   HD21    opls_240    0.380     4<br>&gt;   HD22    opls_240    0.380     4<br>
&gt;      C    opls_235    0.500     5<br>&gt;      O    opls_236   -0.500     5<br>&gt;  [ bonds ]<br>&gt;      N     H<br>&gt;      N    CA<br>&gt;     CA    HA<br>&gt;     CA    CB<br>&gt;     CA     C<br>&gt;     CB   HB1<br>
&gt;     CB   HB2<br>&gt;     CB    CG<br>&gt;     CG   OD1<br>&gt;     CG   ND2<br>&gt;    ND2  HD21<br>&gt;    ND2  HD22<br>&gt;      C     O<br>&gt;     -C     N<br>&gt;  [ dihedrals ] ; override some with residue-specific ones<br>
&gt;      N    CA    CB    CG     dih_ASN_chi1_N_C_C_C<br>&gt;     CG    CB    CA     C     dih_ASN_chi1_C_C_C_CO<br>&gt;     CA    CB    CG   ND2     dih_ASN_chi2_C_C_CO_N<br>&gt;<br>&gt;<br><br>-------------- next part --------------<br>
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<br>------------------------------<br><br>Message: 2<br>Date: Fri, 10 Feb 2012 16:22:18 -0800 (PST)<br>From: MPID &lt;<a href="mailto:mpmcgovern@wisc.edu">mpmcgovern@wisc.edu</a>&gt;<br>Subject: [gmx-users] g_wham with cylinder geometry<br>
To: <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br>Message-ID: &lt;<a href="mailto:1328919738939-4385053.post@n6.nabble.com">1328919738939-4385053.post@n6.nabble.com</a>&gt;<br>Content-Type: text/plain; charset=us-ascii<br>
<br>Hi everyone. I ran an umbrella sampling simulation of a protein in a<br>membrane. I used pull_geometry=cylinder. I tried to analyze the results with<br>g_wham. I got this error:<br><br> Fatal error:<br>With pull geometry &#39;cylinder&#39;, expected pulling in Z direction only.<br>
However, found dimensions [Y Y Y]<br><br>The manual says that with this geometry the pulling is in the direction of<br>pull_vec. I set pull_vec to 0 0 1. Do I have to redo these simulations with<br>a line that says pull_dim = N N Y? Or does the data still mean what it is<br>
supposed to, but g_wham is just giving trouble and I can use a different<br>wham program?<br><br>Here is the pull part of my mdp file:<br><br>pull                     = umbrella<br>pull_geometry            = cylinder<br>pull_r0                  = 2.0<br>
pull_r1                  = 1.5<br>pull_vec1                = 0 0 1<br>pull_start               = yes<br>pull_group0              = DPPGB<br>pull_group1              = PROT<br>pull_k1                  = 500<br>pull_nstxout             = 1000<br>
pull_nstfout             = 1000<br><br><br>--<br>View this message in context: <a href="http://gromacs-users-forum.5086.n6.nabble.com/g-wham-with-cylinder-geometry-tp4385053p4385053.html" target="_blank">http://gromacs-users-forum.5086.n6.nabble.com/g-wham-with-cylinder-geometry-tp4385053p4385053.html</a><br>
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<br>End of gmx-users Digest, Vol 94, Issue 67<br>*****************************************<br></font></span></blockquote></div><br>