[gmx-users] Reg: NPT Equilibration of water
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Fri Oct 29 10:50:13 CEST 2010
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.
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
Regards
Vinoth
On Fri, Oct 29, 2010 at 2:06 PM, Mark Abraham <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> 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>> 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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>>
>> --
>> 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 http://folding.bmc.uu.se
>>
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>
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