Hi Justin Thank you for your comments. Yes i want to concatenate two systems such that their cross sections are same ( X and Y axis length are same for both the boxes) allowing only the Z axis to change. The above procedure was employed in the literature and latter they combined two boxes.
what i want to know ultimately is can i go ahead with this pressure ( i have no problem with temperature and density) for water to create an interface by combining two boxes? Regards Vinoth On Fri, Oct 29, 2010 at 4:21 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > vinothkumar mohanakrishnan wrote: > >> Hi Mark >> >> How come 7 +/- 500 bar is approximately 1 bar. Can you explain it more >> clearly? It will be of more useful to me to understand the concept. >> >> > Suppose you do two simulations. In one, the result is 7+/-500 and in the > other, the result is 1+/-500. Even though the latter achieves the preferred > result (average pressure of 1 bar), statistically, there is no difference > between these two results because of the huge standard deviations in the > data. > > > One more thing, density (from g_energy command) of water is found to low >> (expected 1000) after NPT is equilibration. why? given below is my average >> density value. Can i proceed with this density value? >> >> Energy Average RMSD Fluct. Drift >> Tot-Drift >> >> ------------------------------------------------------------------------------- >> Density (SI) 979.37 14.3238 14.2431 -0.0525784 >> -5.25789 >> > > Real water and SPC water are different. I don't know that there is any > water model out there that perfectly reproduces all the properties of water. > A density around 980 sounds about right for SPC. > > A comment on your previous approach: you're hoping to achieve the same box > dimensions for two different systems in order to concatenate them and make > an interfacial system? It would be far easier to create the organic phase, > extend the box in z, and then solvate with genbox. > > -Justin > > >> Regards >> Vinoth >> >> >> On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham >> <mark.abra...@anu.edu.au<mailto: >> mark.abra...@anu.edu.au>> wrote: >> >> On 29/10/2010 6:39 PM, vinothkumar mohanakrishnan wrote: >> >>> I am using the semiisotropic pressure scaling because i want the >>> box size to remain the same as that of the original box size in X >>> and Y axis and want to change it only on the Z axis. I am doing >>> this because at a latter stage i want to create an interface with >>> organic solvent where i need the cross sections (X and Y axis >>> length) of both the box should be the same. >>> >>> what i should do now get the pressure of 1 bar? >>> >> >> 7 +/- 500 *is* approximately 1 bar, and hardly any better an >> approximation than 1 +/- 500. If you want lower fluctuations, use a >> larger system and run for a much longer time. Or, since you'll have >> to re-equilibrate once you combine the solvent boxes, don't bother. >> >> Mark >> >> >>> Has no one has got the pressure of water to be close to 1 bar in >>> GROMACS till now? >>> >>> Regards >>> Vinoth >>> >>> On Fri, Oct 29, 2010 at 12:54 PM, David van der Spoel >>> <sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se>> wrote: >>> >>> On 2010-10-29 09.08, vinothkumar mohanakrishnan wrote: >>> >>> >>> Hi Mark >>> >>> I read the link before posting the question. even though >>> the fluctation >>> is between 500-600 (as said in the link) bar the average >>> pressure is >>> around 7.4 bar. my concern is the average pressure?. >>> Because at a latter >>> stage i am going to combine this water box with another >>> organic solvent >>> and i want to avoid any complications there. >>> >>> >>> Think again of what you just wrote. Your value is 7 +/- 500. >>> In fact according to normal statistical rules you should round >>> the value of 7 to 0. If you want more accurate number you >>> could increase the box size by a factor of 100. >>> >>> By the way, why are you using semiisotropic pressure scaling >>> in a water box? >>> >>> >>> Regards >>> Vinoth >>> >>> On Fri, Oct 29, 2010 at 12:22 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>>> wrote: >>> >>> On 29/10/2010 5:48 PM, vinothkumar mohanakrishnan wrote: >>> >>> Hi Gromacians >>> >>> I want to do equilibration of water (spc model) >>> first in the NVT >>> ensemble and then in the NPT ensemble to maintain a >>> temperature >>> of 300K and a pressure of 1 bar respectively. The NVT >>> equilibration works fine and the average >>> temperature turns out >>> to be 299.229 K. >>> >>> Energy Average RMSD >>> Fluct. >>> Drift Tot-Drift >>> ------------------------------ >>> ------------------------------------------------- >>> Temperature 299.229 10.3092 >>> 10.2463 >>> 0.0393873 3.93877 >>> Heat Capacity Cv: 12.494 J/mol K (factor = >>> 0.00118698) >>> >>> when i do NPT equilibration i am not getting the >>> desired >>> pressure as 1 bar or atleast close to 1 bar >>> (between 1-1.4 bar). >>> In the mdp file i used semiisotropic pressure >>> coupling type >>> because i want to fix the length of the box same on >>> two axis as >>> that of the original box size and want to change it >>> only on one >>> axis. can any one tell me why iam not getting the >>> desired >>> pressure of 1 bar?. >>> >>> >>> This looks normal for a smallish water system over >>> 100ps. See >>> http://www.gromacs.org/Documentation/Terminology/Pressure >>> >>> Mark >>> >>> >>> >>> Energy Average RMSD >>> Fluct. >>> Drift Tot-Drift >>> >>> >>> ------------------------------------------------------------------------------- >>> Pressure (bar) 7.4339 574.052 >>> 573.574 >>> 0.812129 81.2138 >>> >>> Given below is my mdp file (NPT equilibration). any >>> help is >>> highly appreciated. >>> >>> title = DCE NVT equilibration >>> cpp = usr/bin/cpp >>> integrator = md >>> nsteps = 100000 >>> dt = 0.001 >>> nstxout = 100 >>> nstvout = 100 >>> nstenergy = 100 >>> nstlog = 100 >>> ns_type = grid >>> nstlist = 1 >>> rlist = 1.0 >>> coulombtype = PME >>> rcoulomb = 1.0 >>> vdwtype = Cut-off >>> rvdw = 1.0 >>> pme_order = 4 >>> fourierspacing = 0.16 >>> pbc = xyz >>> tcoupl = V-rescale >>> tc-grps = system >>> tau_t = 0.1 >>> ref_t = 300 >>> pcoupl = berendsen >>> pcoupltype = semiisotropic >>> tau_p = 0.5 >>> ref_p = 1.0 1.0 >>> compressibility = 0.0 4.5e-5 >>> DispCorr = Enerpres >>> gen_vel = yes >>> gen_temp = 300 >>> gen_seed = 173529 >>> >>> Regards >>> Vinoth >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> <mailto:gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org>> >>> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >>> >>> -- David van der Spoel, Ph.D., Professor of Biology >>> Dept. of Cell & Molec. Biol., Uppsala University. >>> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. >>> sp...@xray.bmc.uu.se <mailto:sp...@xray.bmc.uu.se> >>> http://folding.bmc.uu.se >>> >>> >>> -- gmx-users mailing list gmx-users@gromacs.org >>> <mailto:gmx-users@gromacs.org> >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >>> >>> >>> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > 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@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists
