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 <yson...@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 < > sp...@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 <jalem...@vt.edu<mailto: >>>> jalem...@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 >>>> <jalem...@vt.edu <mailto:jalem...@vt.edu> >>>> <mailto:jalem...@vt.edu <mailto:jalem...@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.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au> >>>> <mailto:mark.abra...@anu.edu.au <mailto:mark.abra...@anu.edu.au >>>> >> >>>> <mailto:mark.abra...@anu.edu.au >>>> <mailto:mark.abra...@anu.edu.au> >>>> <mailto:mark.abra...@anu.edu.au >>>> <mailto:mark.abra...@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@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> <mailto:gmx-users@gromacs.org <mailto: >>>> gmx-users@gromacs.org>> >>>> <mailto:gmx-users@gromacs.org >>>> <mailto:gmx-users@gromacs.org> <mailto:gmx-users@gromacs.org >>>> <mailto:gmx-users@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-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@gromacs.org> >>>> <mailto:gmx-users-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@gromacs.org>> >>>> <mailto:gmx-users-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@gromacs.org> >>>> <mailto:gmx-users-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@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@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> <mailto:gmx-users@gromacs.org <mailto: >>>> gmx-users@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-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@gromacs.org> >>>> <mailto:gmx-users-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@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@gromacs.org >>>> <mailto:gmx-users@gromacs.org> >>>> <mailto:gmx-users@gromacs.org <mailto:gmx-users@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-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@gromacs.org> >>>> <mailto:gmx-users-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@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@gromacs.org >>>> <mailto:gmx-users@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-requ...@gromacs.org >>>> <mailto:gmx-users-requ...@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 >>>> >>> >>> >> >> -- >> 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. >> sp...@xray.bmc.uu.se sp...@gromacs.org http://folding.bmc.uu.se >> >> _______________________________________________ >> gmx-users mailing list gmx-users@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-requ...@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 > -- Yanmei Song Ph.D. Candidate Department of Chemical Engineering Arizona State University
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