[gmx-users] shift function for vdwtype and density

[Justin A. Lemkul]

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>> 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     no longer valid.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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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