[gmx-users] increasing cut-off and PME grid spacing

[Justin A. Lemkul]

Hsin-Lin Chiang wrote:
>>If the simulation is even stable, it will be horribly inaccurate.  12 nm cutoffs 
>>are unheard of and 2-nm grid spacing is about 20 times too large.
>>
>>Without seeing the original .mdp file that gave the high PME load, and without a 
>>further description about how large the system is (number of atoms), it is hard 
>>to say what you should do.  Some system do not parallelize well, but I imagine 
>>you should be able to get better performance.
>>
>>-Justin
> 
> 
> 
> Thank you for reply
> 
> The original .mdp is below and the number of atoms is 20171
> 

How big is the box?  You don't have any vacuum space, do you?  The only reason 
I've seen for PME load being so large in conjunction with "normal" settings and 
a simple system is if you've got a large void that causes PME to do a whole lot 
of work to accomplish nothing.

-Justin

> The difference is only in rlist, rcoulomb, rvdw, and fourierspacing
> 
> 
> 
> /title        = ttt
> //cpp                 =  /lib/cpp
> //constraints         =  hbonds
> //;define              =  -DFLEX_SPC
> /i/ntegrator          =  md
> //emtol               =  100.0
> //emstep              =  0.005
> //dt                  =  0.002    ; ps !
> //nsteps              =  25000000  ; total 50 ns
> //nstcomm             =  5000
> //nstxout             =  5000
> //nstvout             =  5000
> //nstfout             =  5000
> //nstlog              =  5000
> //nstenergy           =  5000
> //nstlist             =  10
> //ns_type             =  grid
> 
> //rlist               =  1
> //rcoulomb            =  1
> //rvdw                =  1
> //coulombtype         =  PME
> //fourierspacing      =  0.2
> //pme_order           =  6
> //optimize_fft        =  yes
> //Tcoupl              =  v-rescale
> //tc-grps             =  Protein Non-Protein
> //;tau_t               =  0.1  0.1
> //tau_t               =  0.2 0.2
> //ref_t               =  300 300
> //energygrps          =  A-chain B-chain SOL NA
> //Pcoupl              =  berendsen
> //Pcoupltype          =  isotropic
> //;tau_p               =  0.1
> //tau_p               =  0.25
> //compressibility     =  5.4e-5
> //ref_p               =  1.0
> //gen_vel             =  yes
> //gen_temp            =  300
> //gen_seed            =  173529/
> 
> 
> 
> Hsin-Lin
> 

-- 
========================================

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

========================================