[gmx-users] compressing in presence of voids

[Dallas Warren]

Plus, with such a small number of atoms there is no need to run on more
than a single CPU.  You can even run this one on your workstation for a
significant length of simulation time without any real issue.

Catch ya,

Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.warren at monash.edu
+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail. 

> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-
> bounces at gromacs.org] On Behalf Of Justin A. Lemkul
> Sent: Tuesday, 22 March 2011 1:43 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] compressing in presence of voids
> 
> 
> 
> 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
> >
> 
> --
> ========================================
> 
> 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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