[gmx-users] NPT issue in 4.0.7 and 4.5.3

[Mark Abraham]

On 14/04/2011 10:22 AM, Moeed wrote:
> Hello,
>
> I have run 2 ns simulations on a hydrocarbon system (initial density 
> of ~ 2 SI and box size is 15 nm), one with version 4.0.7 and the other 
> trial using 4.5.3. Both runs are almost equilibrated to 70 bar 
> pressure but one is giving density of above 600SI (4.0.7) and the 
> other density of around 15 SI (4.5.3). With 4.5.3 applying 100 bar 
> pressure does not comrades the system either to the desired density. I 
> need to study the system at different pressures from 1 to 70 bar, and 
> I am wondering if the system can not be compressed with these ref_p 
> values how can I keep the pressure fixed at P < 70 bar!?
>
> Please help if you have any idea on why these two versions are giving 
> inconsistent results and which one is reliable.

Why are your potential energies positive? What does the final 
configuration look like? Why aren't you doing a "simulated annealing" 
style of compression with small increments of delta-P? (These, 
coincidentally are even good data for your study...) Massive leaps in 
ensemble conditions are often poorly-conditioned for numerical 
integration. You're generating velocities that are only approximately 
correct, not giving them any chance to equilibrate, and then smashing 
the system with massive over-pressure. Small wonder it might sometimes 
break...

When reporting output from .log file and g_energy, please either use 
plain text email, or switch to a non-proportional font like Courier. 
Those tables make it harder for people to help you than you want it to be.

Mark

>
> 4.0.7
>
> Statistics over 250001 steps [*1500.0001 thru 2000.0001 ps ],* 14 data 
> sets
> The term 'Cons. rmsd ()' is averaged over 2501 frames
> All other averages are exact over 250001 steps
>
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> -------------------------------------------------------------------------------
> Angle                       36.9945   0.806738   0.804483  0.0521993   
> 0.208798
> Ryckaert-Bell.              9.04227   0.376253   0.371412  0.0521057   
> 0.208424
> LJ-14                       5.23048   0.119612   0.119611 0.00033983 
> 0.00135933
> Coulomb-14                 -1.66329   0.104171   0.102175  0.0175753  
> 0.0703015
> LJ (SR)                    -27.3967          0          0  0.0421934   
> 0.168774
> Coulomb (SR)                8.98711   0.163579    0.16062 -0.0268199   
> -0.10728
> Potential                   31.1944          0          0   0.137594   
> 0.550377
> Kinetic En.                 51.1009   0.987759   0.987724 0.00725949  
> 0.0290381
> Total Energy                82.2953          0          0   0.144851   
> 0.579408
> Temperature                  299.98    5.79849    5.79828 
> 0.000340897   0.170449
> *Pressure (bar)              69.3587    414.279    414.256  
> 0.0298385    14.9193*
> Cons. rmsd ()            4.01744e-06 1.41883e-07 1.41883e-07          
> 0          0
> *Box-X                       3.04882          0          0 3.57512e-06 
> 0.00178757
> Box-Y                       3.04882          0          0 3.57512e-*
>
>
> -----------------------------
> 4.5.3.
>
> [*1500.0001 thru 2000.0001 ps ],*
>
> Energy                      Average   Err.Est.       RMSD  Tot-Drift
> -------------------------------------------------------------------------------
> Angle                       37.1357      0.071   0.812307  -0.099711  
> (kJ/mol)
> Ryckaert-Bell.              9.17677       0.14   0.445934  -0.529281  
> (kJ/mol)
> LJ-14                       5.18878     0.0087   0.137673   -0.03119  
> (kJ/mol)
> Coulomb-14                 -1.60372      0.051   0.126405  -0.144403  
> (kJ/mol)
> LJ (SR)                    -4.24478       0.29   0.742141   0.697187  
> (kJ/mol)
> Coulomb (SR)                8.97451      0.082   0.198278   0.232025  
> (kJ/mol)
> Potential                   54.6272       0.31    1.20733   0.124627  
> (kJ/mol)
> Kinetic En.                 51.1047      0.021     0.9945  -0.066306  
> (kJ/mol)
> Total Energy                105.732       0.31    1.58869   0.058321  
> (kJ/mol)
> Temperature                 300.002       0.12    5.83806  -0.389239  (K)
> *Pressure                     66.734        5.3      91.83    11.5294  
> (bar)*
> Constr. rmsd             2.2661e-10    2.3e-10 3.58302e-08 -1.3595e-09  ()
> *Box-X                       11.0055      0.082   0.175309  -0.496198  
> (nm)
> Box-Y                       11.0055      0.082   0.175309  -0.496198  
> (nm)*
>
>
>
>
>
>
> pbc              =  xyz
>
> integrator          =  md
> dt                  =  0.002
> nsteps              =  1000000
> nstcomm             =  100
> nstenergy           =  100
> nstxout             =  100
>
> nstlist             =  10
> ns_type             =  grid
>
> coulombtype         =  Shift
> vdw-type            =  Shift
> rcoulomb-switch     =  0
> rvdw-switch         =  0.9
> rlist               =  1.2
> rcoulomb            =  1.2
> rvdw                =  1.0
>
> Tcoupl              =  v-rescale
> tc-grps             =  System
> tau_t               =  0.1
> ref_t               =  300
>
>
> Pcoupl              =  berendsen
> Pcoupltype          =  isotropic
> tau_p               =  1
> compressibility     =  4.5e-5 4.5e-5
> ref_p               =  70
>
>
> gen_vel             =  yes
> gen_temp            =  300.0
> gen_seed            =  173529
>
>
> constraints             = all-bonds
> constraint-algorithm = lincs
>

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