[gmx-users] compressing in presence of voids

[Justin A. Lemkul]

Moeed wrote:
> Hello,
> 
> I am compressing a single extended PE chain (16 nm in length) in a box 
> of 20nm in vacuo to get a more realistic shape of the polymer. Although 
> system is small (only 362 atoms), whatever -np #  I choose simulation 
> runs very slowly. Is that because of the presence of voids? Is there a 
> way to speed up the runs? I have no clue on this. Thanks!
> 

PME in vacuo is both extremely slow and unnecessary.  Proper vacuum treatment is 
a non-periodic system with infinite cutoffs (i.e. rlist=rvdw=rcoulomb=0).  You 
shouldn't have to compress this system to get it into a reasonable 
configuration.  The simulations should run extremely fast for such a small 
amount of atoms, allowing you to obtain a nice, long, converged trajectory.

-Justin

> (mpirun -np 4 mdrun_mpi .......    -pd)
> 
> starting mdrun 'Polymer'
> 1000000 steps,   2000.0 ps.
> step 0
> step 100, will finish Thu Mar 24 19:33:34 2011
> step 200, will finish Thu Mar 24 19:29:18 2011
> step 300, will finish Thu Mar 24 19:27:42 2011
> step 400, will finish Thu Mar 24 19:27:13 2011
> step 500, will finish Thu Mar 24 19:27:54 2011
> 
> 
> 
> pbc              =  xyz                  
>        
> ;        Run control                   
> integrator          =  md                    
> dt                  =  0.002                 
> nsteps              =  1000000 ;5000         
> nstcomm             =  100                 
> 
> ;        Output control
> nstenergy           =  100                  
> nstxout             =  100               
> nstvout             =  0
> nstfout             =  0
> nstlog              =  1000               
> nstxtcout          =  1000               
> 
> ;        Neighbor searching
> nstlist             =  10               
> ns_type             =  grid               
> 
> ;        Electrostatics/VdW
> coulombtype         =  PME                    
> vdw-type            =  Shift             
> rcoulomb-switch     =  0                    
> rvdw-switch         =  0.9 ;0               
> 
> ;        Cut-offs
> rlist               =  1.25               
> rcoulomb            =  1.25 ;1.1             
> rvdw                =  1.0               
> 
> ;        PME parameters
> fourierspacing      =  0.12                 
> fourier_nx          =  0
> fourier_ny          =  0
> fourier_nz          =  0
> pme_order          =  4                 
> ewald_rtol          =  1e-5
> ;optimize_fft      =  yes
> 
> ;        Temperature coupling   
> Tcoupl              =  v-rescale               
> tc-grps             =  System        
> tau_t               =  0.1               
> ref_t               =  300           
> 
> ;        Pressure coupling
> Pcoupl              =  berendsen;Parrinello-Rahman            
> Pcoupltype          =  isotropic                
> tau_p               =  0.5       0.5            
> compressibility     =  4.5e-5 4.5e-5       
> ref_p               =  10    10               
> 
> ;        Velocity generation               
> gen_vel             =  yes               
> gen_temp            =  300.0               
> gen_seed            =  173529               
> 
> ;        Bonds
> constraints             = none;all-bonds          
> constraint-algorithm = lincs
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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