Re: [gmx-users] shift function for vdwtype and density

[David van der Spoel]

Justin A. Lemkul wrote:


Yanmei Song wrote:
Dear Justin:

Yes and I tried dispersion correction and it gives a larger density 
than I expected.  The density of the polymer by vdwtype=shift is more 
close to the experimental value. Then your suggestion would be to 
choose the vdwtype=cut-off under this condition even if it result in 
larger density? Thank you so much!


No.  My suggestion is to do your homework, as Mark originally said, and 
as I echoed in my last mail.  Read about the water model, its expected 
performance under different simulation parameters, and evaluate what you 
want to do once you have done this background work.  If you have done a 
thorough literature review, there is no one else that can make a choice 
for you; decide how to handle your system based on what you read.

Actually this is not so easy. Jorgensen has never published the way he 
treats cut-offs, but he was friendly enough to let me know, so we have 
actually done it:
David van der Spoel and Paul J. van Maaren: The origin of layer 
structure artifacts in simulation of liquid water J. Chem. Theor. Comp. 
2 pp. 1-11 (2006)

If you look in the appendix you can find the "one and only" shifting 
method for OPLS. However!!!! This is not to be recommended since the 
effect is very different for MD and MC (what Jorgensen uses). In MD the 
official method will give horrible artifacts. In other words, you have 
to use something better. Our conclusion in the above paper is to use PME 
for Coulomb and not shift Van der Waals. I would also recommend to use 
TIP4P rather than TIP5P, as Jorgensen uses TIP4P for all his 
parameterizations.



-Justin

On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul <jalem...@vt.edu 
<mailto:jalem...@vt.edu>> wrote:



    Yanmei Song wrote:

        Dear Justin:

        Yes. Before I do the water+polymer, I did both the bulk systems
        separately.  The density of TIP5P I mentioned earlier is the
        results for pure water bulk system. My concern is that if it is
        reasonable that the property of the system changes with
        different mdp conditions? Since when I did the bulk water and
        bulk polymer system, I found the densities change with different
        cutoff and vdwtype conditions. Is this a artifact? Or the larger
        cutoff, the more accurate result we can get?


    Every parameter you specify will affect the results you see.  I
    agree with Mark - look up the original reference for TIP5P and see
    what parameters are recommended.  Also read the subsequent
    literature that has used TIP5P to see what modifications
    (electrostatic treatment, vdW treatment, etc) are appropriate or
    even more accurate.

    Also realize that using vdwtype = shift may not be the best
    solution.  I only suggested as a guess for something to try back
    when you were getting bizarre results with your polymer.  Have you
    ever tried dispersion correction when using vdwtype = cutoff?  I
    routinely use such a setup and have never seen any really bizarre
    behavior.

    -Justin

        On Mon, May 18, 2009 at 4:10 PM, Justin A. Lemkul
        <jalem...@vt.edu <mailto:jalem...@vt.edu>
        <mailto:jalem...@vt.edu <mailto:jalem...@vt.edu>>> wrote:



           Yanmei Song wrote:

               Dear Mark:

               Thanks for your answer. I have to use the same mdp file
        for both
               water and another polymer molecules in my system, right?
         Then
               if the shift function works well for the polymer, I can
        not get
               the best result for TIP5P?  The density of TIP5P is 
different
               from the literature value of 982. Thanks!


           So your system is water + polymer?  In that case, you have an
        added
           variable - the interaction between the water and your
        polymer.  What
           you should probably be more concerned with the what the bulk
        density
           of the whole system is.  I have found that analyzing 
densities of
           portions of mixed systems does not give an accurate result.

           -Justin


               On Mon, May 18, 2009 at 3:33 PM, Mark Abraham
               <mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>
        <mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au>>
               <mailto:mark.abra...@anu.edu.au
        <mailto:mark.abra...@anu.edu.au>
               <mailto:mark.abra...@anu.edu.au
        <mailto:mark.abra...@anu.edu.au>>>> wrote:

                  Yanmei Song wrote:

                      Dear All:

                      I found when I changed the vdwtype from cut-off to
        shift, the
                      density of the system decrease significantly.All
        the other
                      setting in the mdp file remain unchanged. For
        example the
                      density of TIP5P water drops to 962. Does it mean
        I can
               not use
                      the shift for vdwtype?


                  Maybe not. Check out the paper in which TIP5P was
               parameterized. The
                  greater the extent to which your .mdp conditions
        differ from
               those
                  conditions, the greater the likelihood that the
               parameterization is
                  no longer valid.

                  Mark
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               --        Yanmei Song
               Ph.D. Candidate
               Department of Chemical Engineering
               Arizona State University


                      
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           --    ========================================

           Justin A. Lemkul
           Ph.D. Candidate
           ICTAS Doctoral Scholar
           Department of Biochemistry
           Virginia Tech
           Blacksburg, VA
           jalemkul[at]vt.edu <http://vt.edu> <http://vt.edu> | (540)
        231-9080

           http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

           ========================================

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        --         Yanmei Song
        Ph.D. Candidate
        Department of Chemical Engineering
        Arizona State University


    --     ========================================

    Justin A. Lemkul
    Ph.D. Candidate
    ICTAS Doctoral Scholar
    Department of Biochemistry
    Virginia Tech
    Blacksburg, VA
    jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
    http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

    ========================================
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--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University



--
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205. Fax: +4618511755.
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