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.
I have generated velocities the step before (in NpT equilibration) and
for the same temperature (200K). So, I would not think this causes the
error as the should be transferred by using the resulting gro-file from
NpT as input for production MD run.
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.
If I repeat it, I should do so with "correct" parameters, I think. Or do
you suggest to repeat it with the very same parameter set as before?
To address the things you mentioned:
- What should or can nstlist be set to?
- 200K have been chosen because at higher temperatures, the test systems
used to move even more.
- Concerning the coupling groups: you mean, I should use a group for
protein and DNA as whole? But isn't restraining the DNA also a
perturbation of the ensemble? At least, I thought that this way the
temperature of the protein should not be affected by the restraints on
the DNA. Tthis was the reason why I put several coupling groups and why
I asked yesterday if it would be better not to couple the restrained DNA
to the thermostate or set its temperature to 0.
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.
That's true. I fear, I will not be able to get it finished till next
week but at least, I can try, start some jobs and see how far I can get.
Thank you very much for your help,
Matthias
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
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