[gmx-users] Pressure coupling and cut-off

[Justin A. Lemkul]

Yanmei Song wrote:
> Dear All:
> 
> I have question about the pressure coupling. I have done a 10ns 
> simulation with 19800 atoms for 120 large molecules using the following 
> pressure coupling.
> 
> Tcoupl              =  berendsen
> tc_grps             =  PDM
> tau_t               =  0.1
> ref_t               =  300
> 
> Pcoupl              =  berendsen
> pcoupltype          =  isotropic
> ;pc-grps            =  PDM
> tau_p               =  1.0
> ref_p               =  1.0
> compressibility     =  4.5e-5
> 
> Then I did g_energy for the last 3ns and got the results:
> 
> Energy                      Average       RMSD     Fluct.      Drift  
> Tot-Drift
> -------------------------------------------------------------------------------
> Potential                    -98061          0          0    0.61668    
> 1850.04
> Temperature                 303.561    109.602    109.602 0.000181791   
> 0.545372
> Pressure (bar)               4.4884    11110.8    11109.8  -0.169835   
> -509.506
> 
> For such a long run the pressure drift is still too much and seem hasn't 
> approached 1bar. Does it mean the system hasn't reach equilibrium yet. I 
> did a similar system by using the same method. it just take 2 or 3ns to 
> reach the equilibrium. and the pressure is around 1.01after the run. The 
> only difference is the cutoff changing from 1.2 to 1.4.  Does the cufoff 
> of 1.4 is too large to make the system running slower. Or the pressure 
> coupling method is not working well.  Anyone can give me any suggestions?
> 
> 

I think it will depend on the interplay of other parameters as well.  Posting a 
complete .mdp file may be more helpful.

-Justin

> -- 
> Yanmei Song
> Ph.D. Candidate
> Department of Chemical Engineering
> Arizona State University
> 
> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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