[gmx-users] compression to study pressure effect
Elisabeth
katesedate at gmail.com
Wed Jun 1 19:43:12 CEST 2011
Dear all,
I am trying to study the effect of pressure on total potential of my system
(8 polymer chains). My problem is that I dont see a systematic effect of
pressure on potentials and I cant judge if different pressures increase or
decrease potential. This is the critical observable in my system and with
high fluctuations I am getting I cant make comment on pressure effect. Total
drift is high in most potential functions..I start my runs from a frame
which is the output of an older NPT run (I use cpt file) that has a close
density to what I want. In the production runs (NPT for 12 27 70 bar).
Below is the settings I am using and I really appreciate it if you could
comment on the most important factors for such a study. I tried different
cutoffs as well...I though maybe increasing cutoffs invloves more
interactions and can represent better the pressure effect...
Thanks so much!
; Run control
integrator = md
dt = 0.002
nsteps = 1000000 ;5000
nstcomm = 100
; Output control
nstenergy = 100
nstxout = 100
nstvout = 0
nstfout = 0
nstlog = 1000
nstxtcout = 1000
; Neighbor searching
nstlist = 10
ns_type = grid
; Electrostatics/VdW
coulombtype = Shift
vdw-type = Shift
rcoulomb-switch = 0.5 ;0
rvdw-switch = 0.9 ;0
; Cut-offs
rlist = 1.32 ;1.25 ; tired different
cutoffs and r -switch...
rcoulomb = 1.1 ;1.0
rvdw = 1.1 ;1.0
; Temperature coupling
Tcoupl = v-rescale
tc-grps = System
tau_t = 0.1
ref_t = 300
; Pressure coupling
Pcoupl = Parrinello-Rahman
Pcoupltype = isotropic
tau_p = 1
compressibility = 3.5e-5
ref_p = 10
; Velocity generation
gen_vel = no;yes
gen_temp = 300.0
gen_seed = 173529
; Bonds
constraints = all-bonds
constraint-algorithm = lincs
results for 12 27 70 bar resp.
Statistics over 2043101 steps [ 500.0000 through 4586.2000 ps ], 17 data
sets
All statistics are over 204311 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
LJ (SR) -634.358 2.9 11.0696 -20.3551
(kJ/mol)
Coulomb (SR) 184.082 1.4 3.62712 9.04046
(kJ/mol)
P*otential 642.528 6.4 23.1897 -44.6636
(kJ/mol)*
Kinetic En. 904.294 0.075 16.2742 0.382223
(kJ/mol)
Total Energy 1546.82 6.3 28.6865 -44.2813
(kJ/mol)
Temperature 300.186 0.025 5.4023 0.126881 (K)
Pressure 12.3856 0.89 887.501 5.41599 (bar)
Density 824.417 2.1 9.27838 14.7965
(kg/m^3)
Statistics over 750001 steps [ 500.0000 through 2000.0000 ps ], 17 data sets
All statistics are over 75001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
LJ (SR) -638.643 4.3 12.0718 -10.2094
(kJ/mol)
Coulomb (SR) 184.51 1 2.89777 5.99117
(kJ/mol)
*Potential 634.902 5.7 22.2857 -21.4761
(kJ/mol)*
Kinetic En. 904.181 0.11 16.2261 -0.275076
(kJ/mol)
Total Energy 1539.08 5.7 27.9661 -21.7511
(kJ/mol)
Temperature 300.148 0.035 5.38636 -0.0913135 (K)
Pressure 27.6467 1.4 881.409 8.58275 (bar)
Density 826.734 3.4 9.76089 6.06824
(kg/m^3)
70 bar run
even 6 ns runs gives large total drifts..e.g.13.4934 for density..
Statistics over 2750001 steps [ 500.0000 through 6000.0000 ps ], 17 data
sets
All statistics are over 275001 points
Energy Average Err.Est. RMSD Tot-Drift
-------------------------------------------------------------------------------
LJ (SR) -639.206 3.7 11.6741 -23.7773
(kJ/mol)
Coulomb (SR) 182.97 1.7 4.18663 11.8694
(kJ/mol)
*Potential 640.114 7.5 24.9191 -51.8187
(kJ/mol)*
Kinetic En. 904.3 0.074 16.2887 0.161695
(kJ/mol)
Total Energy 1544.41 7.5 30.1347 -51.657
(kJ/mol)
Temperature 300.187 0.024 5.40713 0.0536754 (K)
Pressure 69.7658 0.86 893.933 -2.29885 (bar)
Density 829.657 2.3 8.98849 13.4934
(kg/m^3)
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