[gmx-users] shift function for vdwtype and density
Justin A. Lemkul
jalemkul at vt.edu
Tue May 19 01:46:41 CEST 2009
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
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org> <mailto:gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>>
>
>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list.
> Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>>.
>
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> -- Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
>
>
>
> ------------------------------------------------------------------------
>
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search
> before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>
>
> -- ========================================
>
> 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
>
> ========================================
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> <mailto:gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>
> <mailto:gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before
> posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>
>
>
> --
> 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
========================================
More information about the gromacs.org_gmx-users
mailing list