[gmx-users] shift function for vdwtype and density
Yanmei Song
ysong30 at asu.edu
Tue May 19 20:42:44 CEST 2009
Dear all:
This is the mdp I just used for the system. The funny thing is after a 8ns
simulation I got a very high pressure and temperature:
Temperature 343.437
Pressure (bar) 45.782
I also did another run with removing the vdw_switch in mdp and keep all
other condition unchanged. I got good result.
The following is my mdp:
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 20000000 ; total 8ns.
nstcomm = 1
nstxout = 50000
nstvout = 50000
nstfout = 0
nstlog = 5000
nstenergy = 5000
nstxtcout = 25000
nstlist = 10
ns_type = grid
pbc = xyz
coulombtype = PME
vdwtype = Shift
rvdw_switch = 0.8
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.0
fourierspacing = 0.12
pme_order = 4
ewald_rtol = 1e-5
; Berendsen temperature coupling is on in two groups
Tcoupl = berendsen
tc_grps = PDM
tau_t = 0.1
ref_t = 300
; Energy monitoring
energygrps = PDM
; Isotropic pressure coupling is now on
Pcoupl = berendsen
pcoupltype = isotropic
;pc-grps = PDM
tau_p = 1.0
On Tue, May 19, 2009 at 11:12 AM, Yanmei Song <ysong30 at asu.edu> wrote:
> Dear David:
>
> Thank you so much for the valuable information.
>
> "Our conclusion in the above paper is to use PME for Coulomb and not shift
> Van der Waals"
>
> I have read the paper you mentioned and did not find how you treated the
> VdW. Have you done some work on the cut off method for vdw? Since I used PME
> for Coulomb in my system. I am still confusing why not shift for vdw.
>
> " I would also recommend to use TIP4P rather than TIP5P, as Jorgensen uses
> TIP4P for all his parameterizations."
>
> I have read Jorgensen's paper for the OPLS and realized that the TIP4P
> would be the first choice for combining with OPLS. However my concern is
> that TIP4P model is not as good as TIP5P in terms of diffusion constant and
> viscosity which are extremely important for my purpose.
>
> I also have compared SPC and TIP4P and turn out that SPC can give a better
> result for my system. Unfornately SPC has a very bad viscosity as TIP4P. So
> I am trying TIP5P.
>
> Do you think OPLS+ TIP5P can cause serious problem or horrible artifacts.
> If you can suggest some literatures on this that would be great.
>
> I really appericate all your help!
>
> On Mon, May 18, 2009 at 10:37 PM, David van der Spoel <
> spoel at xray.bmc.uu.se> wrote:
>
>> 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.
>>>
>>> Actually this is not so easy. Jorgensen has never published the way he
>> treats cut-offs, but he was friendly enough to let me know, so we have
>> actually done it:
>> David van der Spoel and Paul J. van Maaren: The origin of layer structure
>> artifacts in simulation of liquid water J. Chem. Theor. Comp. 2 pp. 1-11
>> (2006)
>>
>> If you look in the appendix you can find the "one and only"
>
>
>
>> OPLS. However!!!! This is not to be recommended since the effect is very
>> different for MD and MC (what Jorgensen uses). In MD the official method
>> will give horrible artifacts. In other words, you have to use something
>> better. Our conclusion in the above paper is to use PME for Coulomb and not
>> shift Van der Waals. I would also recommend to use TIP4P rather than TIP5P,
>> as Jorgensen uses TIP4P for all his parameterizations.
>>
>>
>>
>>
>> -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
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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> <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 <http://vt.edu> | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
>>>> _______________________________________________
>>>> gmx-users mailing list gmx-users at gromacs.org
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>>>>
>>>>
>>>>
>>>> --
>>>> Yanmei Song
>>>> Ph.D. Candidate
>>>> Department of Chemical Engineering
>>>> Arizona State University
>>>>
>>>
>>>
>>
>> --
>> David van der Spoel, Ph.D., Professor of Biology
>> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>>
>> _______________________________________________
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>
>
>
> --
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
>
--
Yanmei Song
Ph.D. Candidate
Department of Chemical Engineering
Arizona State University
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