On 14/04/2011 10:22 AM, Moeed wrote:
Hello,
I have run 2 ns simulations on a hydrocarbon system (initial density
of ~ 2 SI and box size is 15 nm), one with version 4.0.7 and the other
trial using 4.5.3. Both runs are almost equilibrated to 70 bar
pressure but one is giving density of above 600SI (4.0.7) and the
other density of around 15 SI (4.5.3). With 4.5.3 applying 100 bar
pressure does not comrades the system either to the desired density. I
need to study the system at different pressures from 1 to 70 bar, and
I am wondering if the system can not be compressed with these ref_p
values how can I keep the pressure fixed at P < 70 bar!?
Please help if you have any idea on why these two versions are giving
inconsistent results and which one is reliable.
Why are your potential energies positive? What does the final
configuration look like? Why aren't you doing a "simulated annealing"
style of compression with small increments of delta-P? (These,
coincidentally are even good data for your study...) Massive leaps in
ensemble conditions are often poorly-conditioned for numerical
integration. You're generating velocities that are only approximately
correct, not giving them any chance to equilibrate, and then smashing
the system with massive over-pressure. Small wonder it might sometimes
break...
When reporting output from .log file and g_energy, please either use
plain text email, or switch to a non-proportional font like Courier.
Those tables make it harder for people to help you than you want it to be.
Mark
4.0.7
Statistics over 250001 steps [*1500.0001 thru 2000.0001 ps ],* 14 data
sets
The term 'Cons. rmsd ()' is averaged over 2501 frames
All other averages are exact over 250001 steps
Energy Average RMSD Fluct. Drift
Tot-Drift
-------------------------------------------------------------------------------
Angle 36.9945 0.806738 0.804483 0.0521993
0.208798
Ryckaert-Bell. 9.04227 0.376253 0.371412 0.0521057
0.208424
LJ-14 5.23048 0.119612 0.119611 0.00033983
0.00135933
Coulomb-14 -1.66329 0.104171 0.102175 0.0175753
0.0703015
LJ (SR) -27.3967 0 0 0.0421934
0.168774
Coulomb (SR) 8.98711 0.163579 0.16062 -0.0268199
-0.10728
Potential 31.1944 0 0 0.137594
0.550377
Kinetic En. 51.1009 0.987759 0.987724 0.00725949
0.0290381
Total Energy 82.2953 0 0 0.144851
0.579408
Temperature 299.98 5.79849 5.79828
0.000340897 0.170449
*Pressure (bar) 69.3587 414.279 414.256
0.0298385 14.9193*
Cons. rmsd () 4.01744e-06 1.41883e-07 1.41883e-07
0 0
*Box-X 3.04882 0 0 3.57512e-06
0.00178757
Box-Y 3.04882 0 0 3.57512e-*
-----------------------------
4.5.3.
[*1500.0001 thru 2000.0001 ps ],*
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
Angle 37.1357 0.071 0.812307 -0.099711
(kJ/mol)
Ryckaert-Bell. 9.17677 0.14 0.445934 -0.529281
(kJ/mol)
LJ-14 5.18878 0.0087 0.137673 -0.03119
(kJ/mol)
Coulomb-14 -1.60372 0.051 0.126405 -0.144403
(kJ/mol)
LJ (SR) -4.24478 0.29 0.742141 0.697187
(kJ/mol)
Coulomb (SR) 8.97451 0.082 0.198278 0.232025
(kJ/mol)
Potential 54.6272 0.31 1.20733 0.124627
(kJ/mol)
Kinetic En. 51.1047 0.021 0.9945 -0.066306
(kJ/mol)
Total Energy 105.732 0.31 1.58869 0.058321
(kJ/mol)
Temperature 300.002 0.12 5.83806 -0.389239 (K)
*Pressure 66.734 5.3 91.83 11.5294
(bar)*
Constr. rmsd 2.2661e-10 2.3e-10 3.58302e-08 -1.3595e-09 ()
*Box-X 11.0055 0.082 0.175309 -0.496198
(nm)
Box-Y 11.0055 0.082 0.175309 -0.496198
(nm)*
pbc = xyz
integrator = md
dt = 0.002
nsteps = 1000000
nstcomm = 100
nstenergy = 100
nstxout = 100
nstlist = 10
ns_type = grid
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch = 0
rvdw-switch = 0.9
rlist = 1.2
rcoulomb = 1.2
rvdw = 1.0
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
Pcoupl = berendsen
Pcoupltype = isotropic
tau_p = 1
compressibility = 4.5e-5 4.5e-5
ref_p = 70
gen_vel = yes
gen_temp = 300.0
gen_seed = 173529
constraints = all-bonds
constraint-algorithm = lincs
--
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