[gmx-users] Effect of refcoord_scaling

[Christopher Neale]

The problem could be gen_vel=no if you are not loading velocities that are consistent with your production temperature of 200 K. If, for example, you do not load any velocities at all, then the initial forces will quickly be scaled up to reach 200 K and this can cause large scale deformations/rearrangements.

There are a number of other strange things (like nstlist=5 with dt=0.0005 -- nstlist seems unnecessarily frequent, the 200 K temperature, and your use of separate temperature coupling groups which does not give the correct ensemble). Still, those are tangents to your main question.

Nevertheless, if you don't have time to run any more simulations (as you stated earlier) then none of this is really going to help you. If, on the other hand, you do have time to run other simulations, then I still think you should start with repeating your result.

Chris.

 -- original message --

I guess you want to see the production mdp file. Here it is:


; VARIOUS PREPROCESSING OPTIONS
title                    = Production Simulation
cpp                      = /lib/cpp
define                   = -DPOSRES_DNA

; RUN CONTROL PARAMETERS
integrator               = md
tinit                    = 0       ; Starting time
dt                       = 0.0005 ; 2 femtosecond time step for integration
nsteps                   = 100000000

; OUTPUT CONTROL OPTIONS
nstxout                  = 50000 ; Writing full precision coordinates 
every nanosecond
nstvout                  = 50000 ; Writing velocities every nanosecond
nstfout                  = 0     ; Not writing forces
nstlog                   = 5000  ; Writing to the log file every step
nstenergy                = 5000  ; Writing out energy information every step
nstxtcout                = 5000  ; Writing coordinates every 5 ps
energygrps               = Protein DNA water_and_ions

; NEIGHBORSEARCHING PARAMETERS
nstlist                  = 5
ns-type                  = Grid
pbc                      = xyz
rlist                    = 0.9

; OPTIONS FOR ELECTROSTATICS AND VDW
coulombtype              = Reaction-Field
rcoulomb                 = 1.4
epsilon_rf               = 78
epsilon_r                = 1
vdw-type                 = Cut-off
rvdw                     = 1.4

; Temperature coupling
Tcoupl                   = Berendsen
tc-grps                  = Protein  DNA   water_and_ions
tau_t                    = 0.1      0.1      0.1
ref_t                    = 200      200   200
; Pressure coupling
Pcoupl                   = Berendsen
Pcoupltype               = Isotropic
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0

; GENERATE VELOCITIES FOR STARTUP RUN
gen_vel                  = no

; OPTIONS FOR BONDS
constraints              = all-bonds
constraint-algorithm     = Lincs
unconstrained-start      = yes
lincs-order              = 4
lincs-iter               = 1
lincs-warnangle          = 30


Thanks for your help,
Matthias