[gmx-users] Conserved Energy in csvr NVT runs

[janos.daru]

Dear All,

I run simple md job (GMX version:4.6.5 double precision) for
alanine-dipeptid with careful options.
nstlist                  = 1
ns_type               = simple
pbc                     = no
rlist                     = 0
epsilon_r                = 1
coulombtype          = cut-off
rcoulomb                 = 0
vdwtype                  = cut-off
rvdw                     = 0  
dispcorr                 = no
constraints              = h-bonds
constraint-algorithm     = Lincs
lincs-order              = 4
lincs-iter               = 2

For NVE runs I get very nice conserved energy values: ~10E-5
K/numberOfDegreesOfFreedom/ps

But when I change to v-rescale with the following settings, I get clear
drift(~1 K/numberOfDegreesOfFreedom/ps).

tcoupl                   = v-rescale          
tc-grps                  = Protein
tau_t                    = 0.05       
ref_t                    = 300         
nsttcouple               = 1

As total energy and temperature makes a proper oscillation I have the
filling, that "Conserved Energy" is not calculated as I expected, or I miss
something important form the input.

An other observation is that in NVE runs I need to use comm_mode=none to get
nice energy conservation, while in NVT I get slightly better results with
comm_mode=angular for longer runs (aprox 2.5 ns).

Could some experienced user comment on these observations and give me
advice, how to proceed to get proper NVT ensamble without artifacts of the
drift?

I didn't find in the manual options for global and local thermostats. Can I
use local (each degrees of freedom) thermostat in gromacs?

Thank you in advance,

Janos 





--
View this message in context: http://gromacs.5086.x6.nabble.com/Conserved-Energy-in-csvr-NVT-runs-tp5015881.html
Sent from the GROMACS Users Forum mailing list archive at Nabble.com.