<br>Dear gromacs users,<br><br> I went through the papers <a href="http://dx.doi.org/10.1021/jp003919d" target="_blank">dx.doi.org/10.1021/jp003919d</a>. on OPLS,<br>Its is stated in the paper<br><br>&quot;Intermolecular interactions were truncated at 11 Å, with the standard <br>
correction for the interactions beyond that radius. The electrostatic <br>interactions were quadratically feathered to zero over the last 0.5 Å <br>before the cutoff distance.&quot;<br><br><br>another OPLS reference <br>&quot;Optimized Intermolecular Potential Functions for Liquid<br>
Hydrocarbons&quot; - J. Am. Chem. Soc. 1984, 106, 6638-6646<br><br>&quot;In most cases, the intermolecular nonbonded interactions were truncated<br>at 11 Å based on roughly the center-of-mass separations with quadratic<br>
smoothing of the interaction energy to zero over the last 0.5 Å. The cutoff<br>for alkenes and acetals was 13 Å, while for propanol, cyclohexane,<br>2-methyl-2-propanol, phenol, ethyl methyl sulfide, NMA, DMA, and NMP it was <br>
extended to 15 Å.&quot;<br><br>So from these and other references of OPLS - AA force field, is it possible to<br>set a range for vdw, coulomb interactions, so that we can use in that range <br>according to the system we are working on?<br>
<br>Pardon me if the question is wrong. Your references and books will be of<br>great help for me.<br><br>Can anyone suggest regarding the preference of vdw_type (cutoff/shift or <br>
switch),<br><br>Thank you <br>MKS<br><br><br><br> <br><br> <br><div class="gmail_quote">On Sat, Jan 22, 2011 at 11:18 PM, Justin A. Lemkul <span dir="ltr">&lt;<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>&gt;</span> wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im"><br>
<br>
Kavyashree M wrote:<br>
<blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;">
I went through few papers related to OPLS-AA, but could not find<br>
any specific values mentioned for vdw and coulomb intecations..<br>
In one of the papers<br>
&quot;.....In most cases, the intermolecular nonbonded interactions were<br>
truncated at 11Å based on roughly the center-of-mass separations<br>
with quadratic smoothing of the interaction energy to zero over the<br>
last 0.5 Å. The cutoff for alkenes and acetals was 13 Å, while for<br>
propanol, cyclohexane, 2-methyl-2-propanol, phenol, ethyl methyl<br>
sulfide, NMA, DMA, and NMP it was extended to 15 Å.....&quot;<br>
J. Am. Chem. Soc. 1996, 118, 11225-11236.<br>
<br>
</blockquote>
<br></div>
That is an older version of OPLS.  See <a href="http://dx.doi.org/10.1021/jp003919d" target="_blank">dx.doi.org/10.1021/jp003919d</a>.  The cutoffs are much clearer.<br><font color="#888888">
<br>
-Justin<br>
<br>
</font><blockquote class="gmail_quote" style="margin: 0pt 0pt 0pt 0.8ex; border-left: 1px solid rgb(204, 204, 204); padding-left: 1ex;"><div class="im">
<br>
So does this cut off refer to coulombic interactions?<br>
is it correct if iI use the following parameters for OPLS-AA force field?<br>
<br>
-----------------------------------------------------------------------------<br>
;NEIGHBOUR SEARCHING<br>
nstlist         = 10                    ; FREQUENCY WITH WHICH NEIGHBOURLIST IS UPDATED<br>
ns_type         = grid                  ; TYPE OF NEIGHBOUR SEARCH GRID OR SIMPLE<br>
pbc             = xyz                   ; DIRECTION OF PERIODIC BOUNDARY CONDITIONS USAGE<br>
rlist           = 1.4                  ; CUT-OFF DISTANCE FOR SHORT RANGE NEIGHBOUR LIST<br>
<br>
;ELECTROSTATICS<br>
coulombtype     = PME                   ; METHOD FOR CALCULATING COULOMIC INTERCATION - PARTICLE MESH EWALD<br>
rcoulomb        = 1.4                  ; CUTOFF DISTANCE FOR ELECTROSTATIC INTERACTIONS<br>
epsilon_r       = 1                     ; RELATIVE DIELECTRIC CONSTANT<br>
<br>
;VAN DER WAALS<br>
vdwtype         = Switch                ; METHOD FOR TREATING VANDERWAAL&#39;S FORCES<br>
rvdw_switch     = 0.9<br>
rvdw            = 1.00                  ; CUTOFF DISTANCE FOR LJ OR BUCKINGHAM INTERACTIONS<br>
--------------------------------------------------------------------------------------------------------------------<br>
<br>
<br>
Thanks<br>
MKS<br>
<br>
<br></div><div class="im">
On Sat, Jan 22, 2011 at 6:41 PM, Justin A. Lemkul &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt; wrote:<br>

<br>
<br>
<br>
    Kavyashree M wrote:<br>
<br>
        Sir,<br>
<br>
            Yes sir I am using PME. And one more thing I noticed was,<br>
        the protein has<br>
        7 disulphide bonds, so when I reduce all the cystine to cysteine<br>
        or to alanine,<br>
        the the sum of charge group radii reduces from 0.31..nm to<br>
        0.30..nm and also the<br>
        value of this is identical in case of alanine mutation or<br>
        cysteine mutation.<br>
           I finalised on the value of rlist = rcolomb = 1.35nm so as<br>
        not to take risk.<br>
        is that fine?<br>
         <br>
<br>
    As I said before, read the OPLS paper.  1.35 nm does not sound right.<br>
<br>
    -Justin<br>
<br>
        Thank you<br>
        M. Kavyashree<br>
<br>
<br>
        On Sat, Jan 22, 2011 at 6:26 PM, Justin A. Lemkul<br>
        &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br></div><div><div></div><div class="h5">
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
           Kavyashree M wrote:<br>
<br>
               Sir,<br>
<br>
                   System is a protein with 123 aa. No modifications<br>
        were made<br>
               on the pdb file,<br>
               and it was submitted to pdb2gmx by removing all HETATMs,<br>
               retaining only protein<br>
               atoms. topology was created entirely by pdb2gmx and no other<br>
               molecule was introduced.<br>
<br>
                   I will go through the OPLSAA paper, but if I increase<br>
        rlist<br>
               to 1.4nm without reducing<br>
               rvdw according to &quot;The Origin of Layer Structure Artifacts in<br>
               Simulations of Liquid Water&quot;<br>
               - JCTC, 2006, 2, 1-11, will it not cause orderedwater shell<br>
               during simultion?<br>
<br>
<br>
           You&#39;re using PME.  In the first paragraph of the<br>
        introduction, it is<br>
           stated that the spurious effect does not occur with PME.<br>
<br>
           -Justin<br>
<br>
<br>
               Thanking you<br>
               M. Kavyashree<br>
<br>
<br>
               On Sat, Jan 22, 2011 at 12:27 AM, Justin A. Lemkul<br>
               &lt;<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;<br>
               &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;<br>
        &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> &lt;mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>&gt;&gt;&gt;&gt; wrote:<br>
<br>
<br>
<br>
                  Kavyashree M wrote:<br>
<br>
                      Sir,<br>
<br>
                        What exactly can be wrong with the topology? As<br>
        I tried<br>
               with<br>
<br>
<br>
                  I don&#39;t know, what&#39;s in your system?  Was the topology<br>
        created<br>
                  entirely by pdb2gmx, or have you introduced some other<br>
        molecules<br>
                  that you&#39;ve parameterized?<br>
<br>
<br>
                      different PDBs of same structure at higher resolutions<br>
               too, I am<br>
                      getting<br>
                      almost similar charge group radii, so can you kindly<br>
               elaborate about<br>
                      what can go wrong in the topology to get such values?<br>
<br>
<br>
                  Large charge groups indicate that a fair number of<br>
        atoms have<br>
               been<br>
                  included in the same charge group.  Usually only two<br>
        or three<br>
               atoms<br>
                  are in a charge group, rendering them fairly small.  With<br>
               PME, the<br>
                  effects may not be that large, i.e.<br>
                                <a href="http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html" target="_blank">http://lists.gromacs.org/pipermail/gmx-users/2010-November/056219.html</a>,<br>
                  but it&#39;s still worth investigating what your largest<br>
        charge<br>
               group is<br>
                  that&#39;s causing this problem.  If the topology is sound<br>
        and is<br>
               based<br>
                  entirely upon standard force field files, it may<br>
        suffice to<br>
               simply<br>
                  increase rlist to 1.4 nm, leaving all the other<br>
        cutoffs at 1.0,<br>
                  which I believe is standard for OPLS (but don&#39;t just<br>
        take my word<br>
                  for it).<br>
<br>
                  -Justin<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 href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt;<br>
        &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
<br>
               231-9080<br>
<br>
                  <a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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           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 href="http://vt.edu" target="_blank">vt.edu</a> &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; &lt;<a href="http://vt.edu" target="_blank">http://vt.edu</a>&gt; | (540)<br>
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    Ph.D. Candidate<br>
    ICTAS Doctoral Scholar<br>
    MILES-IGERT Trainee<br>
    Department of Biochemistry<br>
    Virginia Tech<br>
    Blacksburg, VA<br>
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</div></div></blockquote><div><div></div><div class="h5">
<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 href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
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