[gmx-users] Reg: NPT Equilibration of water
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 29 13:58:41 CEST 2010
vinothkumar mohanakrishnan wrote:
> Hi Justin
>
> Thank you. One more question regarding the Compressibility value usage.
> can i use the Compressibility value of water (4.5e-5) for the NPT
> equilibration of organic liquids (say DCE)? Is it resonable?
>
> It was said in the gromacs mailing archive that for all liquids one can
> use the Compressibility value of water.
> (http://www.mail-archive.com/gmx-users@gromacs.org/msg01245.html)
>
Yes, it's fine. When a lead developer and the manual (section 3.4.9) indicate
that it is true, I would have no reason to second-guess it...
-Justin
> Regards
> Vinoth
>
> On Fri, Oct 29, 2010 at 4:42 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
>
>
>
> vinothkumar mohanakrishnan wrote:
>
> 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?
>
>
>
> Yes, it's fine. Regardless, you're going to have to do more
> equilibration after you've assembled the system.
>
> -Justin
>
> Regards
> Vinoth
>
>
> On Fri, Oct 29, 2010 at 4:21 PM, Justin A. Lemkul
> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> <mailto:jalemkul at vt.edu <mailto:jalemkul at 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.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:
>
> 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
> <spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>
> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at 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.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>>>
> <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
> <mailto:Mark.Abraham at 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 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>>>
> <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
> <mailto:gmx-users at 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-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>>>
> <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
> <mailto:gmx-users-request at 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.
> spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>
> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se> <mailto:spoel at xray.bmc.uu.se
> <mailto:spoel at xray.bmc.uu.se>>>
>
> http://folding.bmc.uu.se
>
>
> -- 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://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-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/Support/Mailing_Lists
>
>
>
>
> --
> 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://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-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/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 <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://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-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/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 <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://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-request at gromacs.org
> <mailto:gmx-users-request at 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
========================================
More information about the gromacs.org_gmx-users
mailing list