[gmx-users] Reg: NPT Equilibration of water
vinothkumar mohanakrishnan
kmvinoth at gmail.com
Fri Oct 29 09:39:15 CEST 2010
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?
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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