[gmx-users] shift function for vdwtype and density
Yanmei Song
ysong30 at asu.edu
Tue May 19 01:41:44 CEST 2009
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!
On Mon, May 18, 2009 at 4:29 PM, Justin A. Lemkul <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>> 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>>> 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> | (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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