[gmx-users] System instability with switched cut-off

[Berk Hess]

Hi,

Never ever use switched cut-off's!
Switched cut-off's can give extremely strong artifacts.
In 4.1 grompp will warn you about this.

Switch gives you correct energies at short range, but incorrect forces
in the switching region.
What you want is correct forces up to (nearly) the cut-off.
Shift does this.
But reaction-field does this smoother and it even has a physical interpretation.
So use RF if you can not use PME.

But why can't you use PME, you have pbc, right?

Berk


From: matteus.lindgren at chem.umu.se
To: gmx-users at gromacs.org
Date: Fri, 7 Aug 2009 13:13:24 +0200
Subject: [gmx-users] System instability with switched cut-off
















Dear all

 

Im trying to extract the interaction
energies between protein and solvent. Since PME cant be used for this, plain
cutoffs causes problems and shifted cut-offs gives incorrect energies I want to
use switched cutoff but with rather long cutoffs to get the correct energy. 

 

Unfortunately my system is unstable and
within a few ps the total energy and kinetic energy fluctuates several hundred
per cent. I´ve tried different options but can´t get it to stabilize except if
I´m using any other coulomb type. Any ideas?

 

title                    =
Dyna

cpp                      =
/usr/bin/cpp

constraints              =
hbonds

integrator               =
md

dt                       =
0.002

nsteps                   =
20000000

nstxout                  =
20000000

nstvout                  =
20000000

nstfout                  =
5000

nstlog                   =
250

nstenergy                =
500

nstxtcout                =
500

xtc_grps                 = 

energygrps               =
polar hydrophobic peptide  SOL 

nstlist                  = 1

ns_type                  =
grid

coulombtype              =
switch

rcoulomb_switch          =
1.4

rcoulomb                 =
1.7

rlist                    =
2.0

vdwtype                  =
switch

rvdw_switch              =
1.4

rvdw                     =
1.7

tcoupl                   =
nose-hoover

tc-grps                  = Protein   
Non-Protein

tau_t                    =
0.5  0.5

ref_t                    =
298    298

Pcoupl                   =
parrinello-rahman

tau_p                    =
1.0

compressibility          =
4.5e-5

ref_p                    =
1.0

 

;disre_fc                 =
30

 

gen_vel                  = yes

gen_temp                 = 298

gen_seed                 = 173529

unconstrained_start     
= no

 

Thanks

Matteus 

 

--------------------------------------------------------- 

Matteus
Lindgren, graduate student

Department of Chemistry, Umeå University 

SE-901 87 Umeå, Sweden

Phone:  +46 (0)90-7865368  

 

 


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