[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
>>> _______________________________________________
>>> 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/searchbefore
>>> 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
>
> ========================================
> _______________________________________________
> gmx-users mailing list 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.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090518/8ac304f5/attachment.html>
More information about the gromacs.org_gmx-users
mailing list