[gmx-users] Reg: NPT Equilibration of water
Justin A. Lemkul
jalemkul at vt.edu
Fri Oct 29 12:51:11 CEST 2010
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>> 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>> 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>>> 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
>>
>>
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>> Dept. of Cell & Molec. Biol., Uppsala University.
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--
========================================
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
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