[gmx-users] shift function for vdwtype and density

Yanmei Song ysong30 at asu.edu
Tue May 19 01:04:53 CEST 2009

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!

On Mon, May 18, 2009 at 3:33 PM, Mark Abraham <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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