[gmx-users] Reg: NPT Equilibration of water

[Mark Abraham]

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
>