[gmx-users] pressure scaling more than 1%

[Justin A. Lemkul]

Sebastian Waltz wrote:
> Hi all,
> 
> my simulation runs well for the first 700000 steps with a
> step size of 0.001ps and when I get the warning that the
> pressure scaling is more than 1% every 10000 step or so.
> So, is my tau_p of 0.2 to small or is the equillibration
> not done well enough.

Possibly, have you tried larger values?  Usually something on the order of 
1.0-5.0 ps is more typical.

> I am simulating a small peptide in CHCl3 with an handmade
> CHCl3 model. 
> 

If you're seeing instabilities, it could also be related to the topology.  Have 
you thoroughly validated the parameters you're using for CHCl3?

-Justin

>  title        = ttt
> cpp                 =  /lib/cpp
> include             = -I../top
> constraints         =  none
> ;define              =  -DFLEX_SPC
> ;define              =  -DPOSRES			; for possition
> restraints
> integrator          =  md			
> emtol               =  100.0 			
> emstep              =  0.005			
> dt                  =  0.001    		; ps !
> nsteps              =  2000000  		; total 2 ns
> nstcomm             =  1			
> 
> nstxout             =  0			
> nstvout             =  0			
> nstfout             =  10			
> nstlog              =  0			
> nstenergy           =  10			
> nstxtcout           =  10
> 
> xtc_grps            = Protein+PTS+AIC 
> 
> nstlist             =  5			
> ns_type             =  grid			
> rlist               =  1.2			
> 
> coulombtype         =  PME			
> rcoulomb            =  1.2			
> rvdw                =  1.2			
> fourierspacing      =  0.12			
> pme_order           =  4			
> optimize_fft        =  yes
> 
> Tcoupl              =  berendsen
> tc-grps             =  Protein+PTS+AIC CHCl3
> tau_t               =  0.1 0.1 
> ref_t               =  300 300
> 
> energygrps          =  Protein+PTS+AIC CHCl3
> 
> Pcoupl              =  berendsen
> tau_p               =  0.2
> compressibility     =  5.4e-5
> ref_p               =  1.0
> 
> gen_vel             =  yes
> gen_temp            =  300
> gen_seed            =  913529
> 
> 
> Thanks

-- 
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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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