[gmx-users] shift function for vdwtype and density

Yanmei Song ysong30 at asu.edu
Tue May 19 05:05:23 CEST 2009


Dear Justin:

Thanks so much for your effort and information. Perhaps I did not set the
proper value for vdw_switch. I will try some value. I really appreciate your
nice help!

On Mon, May 18, 2009 at 5:24 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
> Perhaps I can contribute something else that might be a bit more useful.
>  It just occurred to me that if you are only changing the vdwtype parameter,
> then you are not correctly implementing the shift function.  See here for
> proper use of a shift potential:
>
> http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#vdw
>
> Take note of the necessary changes to vdw_shift, and potentially rlist.  A
> few quick tests of the shift function indicate the following:
>
> Case 1. Plain cutoff's at 1.2 nm
> Density: 988 kg/m^3
>
> Case 2. Shift potential (no other changes, i.e. rvdw_switch = 0, rvdw =
> 1.2)
> Density: 962 kg/m^3
>
> Case 3. More appropriate shift potential (rvdw_switch = 1.0, rvdw = 1.2)
> Density: 983 kg/m^3
>
> -Justin
>
>
> 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.
>>
>> -Justin
>>
>>  On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul <jalemkul at vt.edu<mailto:
>>> jalemkul at 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
>>>        <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>>>        <mailto:jalemkul at vt.edu <mailto:jalemkul at 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.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>
>>>        <mailto:Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>
>>>               <mailto:Mark.Abraham at anu.edu.au
>>>        <mailto:Mark.Abraham at anu.edu.au>
>>>               <mailto:Mark.Abraham at anu.edu.au
>>>        <mailto:Mark.Abraham at 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
>>>
>>
>>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]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
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