[gmx-users] Reg: NPT Equilibration of water

[vinothkumar mohanakrishnan]

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.

Regards
Vinoth

On Fri, Oct 29, 2010 at 12:22 PM, Mark Abraham <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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