[gmx-users] Re: Unsteady Density
Vitaly Chaban
vvchaban at gmail.com
Mon May 2 20:54:45 CEST 2011
>
>
> I have been trying to use CHARMM forcefield to simulate 1000 molecules
> of Methanol in a box but I seem to fall short on the density every
> time I run. At first, I had my rlist at 1 but CHARMM recommends
> greater than 1.2-1.4 nm so I changed accordingly, then I changed it so
> that the short neighbor list would update more freqently and finally I
> even added a greater amount of steps, hoping that the pressure and
> density would settle down at some value.
>
> Below, I had taken and modified from the Lysozyme tutorial. One thing
> I noticed is the contraint -algorithm and how the constraints are set
> to 'all-bonds'. Is this necessary? After running NVT (leveled off
> near 298K, seemed ok), then NPT, for 300,000 steps, the pressure is
> close to the reference 1 bar, ~1.1,1.2 bar, but I noticed the density
> is still oscillating, not by much, but it still leaves me questioning
> why its not settling around to the literature value of 0.791 g/cm3. I
> posted the last several lines from the analysis *.xvg file. NPT
> script is also below.
>
> Is there still more steps that I have to run for? The density just
> seems to be oscillating too much and although a literature value of
> 0.791 g/cm3 is within the data, it doesnt seem to be settling around
> that value. I have similar problems for 1-propanol to where my
> simulated density is under that of the literature value. Could it be
> possible that maybe I should use different NVT, NPT algorithms
> (tcoupl, pcoupl)?
>
> I would really appreciate anyones help. I'm still in my first few
> months of learning the program. Thanks!
>
> 591.800000 38039.125000 297.409546 -206.071747 779.428894
> 592.000000 38035.421875 294.951111 -20.557419 777.816956
> 592.200000 37982.812500 298.063324 -463.192047 776.430542
> 592.400000 37681.421875 295.430878 36.529854 776.460876
> 592.600000 37476.148438 297.193787 -28.961288 775.634644
> 592.800000 37611.574219 297.059875 -553.369263 774.096924
> 593.000000 37682.277344 288.297974 -293.567963 776.055237
> 593.200000 37147.824219 295.985901 -221.989441 781.570679
> 593.400000 37404.906250 293.938721 399.093018 788.921570
> 593.600000 37339.914062 297.464783 415.891235 793.838440
> 593.800000 37909.019531 292.707184 574.818726 796.730286
> 594.000000 37369.820312 304.095703 -119.569496 796.235962
> 594.200000 37293.445312 294.449005 -63.335049 794.578552
> 594.400000 37196.917969 295.323761 104.148239 791.275085
> 594.600000 37776.199219 298.004333 28.989655 785.244629
> 594.800000 37893.097656 302.397308 -268.065765 779.457886
> 595.000000 38123.460938 295.343109 -140.914047 775.682678
> 595.200000 38002.054688 302.233124 -91.893478 774.813660
> 595.400000 37835.652344 297.808319 441.931885 776.142090
> 595.600000 38103.964844 296.369019 490.766754 778.422302
> 595.800000 37686.902344 303.358093 -19.726471 781.057922
> 596.000000 37586.890625 293.751648 -92.387199 783.724854
> 596.200000 37408.414062 300.007385 -288.156036 785.990417
> 596.400000 37894.898438 295.720520 346.861206 788.753174
> 596.600000 37673.378906 288.311432 89.059952 789.179993
> 596.800000 36881.062500 295.265564 70.789131 791.552673
> 597.000000 37077.789062 296.261444 72.207787 793.970398
> 597.200000 37123.230469 296.511475 -232.434616 793.653564
> 597.400000 37426.152344 304.281891 -133.300797 791.791077
> 597.600000 37514.332031 305.183197 -259.364136 787.592712
> 597.800000 37393.667969 301.326111 -150.162338 785.053711
> 598.000000 37263.054688 299.811554 326.851837 785.553894
> 598.200000 37203.261719 300.688904 225.526001 788.008667
> 598.400000 37511.636719 302.506714 66.299194 790.725281
> 598.600000 37460.843750 299.512909 198.943665 793.353333
> 598.800000 37248.921875 291.575134 -93.283127 793.582703
> 599.000000 36870.480469 293.515381 211.069107 792.929443
> 599.200000 37398.097656 293.184448 -163.371140 789.150513
> 599.400000 37402.238281 297.402008 45.650658 786.303711
> 599.600000 37419.816406 298.520508 -147.688004 783.492371
> 599.800000 37497.332031 296.529877 -15.991615 782.294250
> 600.000000 37691.468750 298.839844 -68.580627 781.974182
>
>
>
> title =Methanol npt equilibration
>
> ;Run parameters
> integrator =md ;leap-frog algorithm
> nsteps =300000 ;2 * 50000 = 100 ps
> dt =0.002 ;2fs
>
> ;Output control
> nstxout =100 ;save coordinates every 0.2 ps
> nstvout =100 ;save velocities every 0.2 ps
> nstenergy =100 ;save energies every 0.2 ps
> nstlog =100 ;update log file every 0.2 ps
>
> ;Bond parameters
> continuation =yes ;Restarting after NVT
> constraint_algorithm=lincs ;holonomic constraints
> constraints =all-bonds ;all bonds (even heavy atom-H
> bonds)constraind
> lincs_iter =1 ;accuracy of LINCS
> lincs_order =4 ;also related to accuracy
>
> ;Neighborhood searching
> ns_type =grid ;search neighboring grid cells
> nstlist =1 ;2 fs
> rlist =1.4 ;short-range neighborlist cutoff
> (in nm)
> rcoulomb =1.4 ;short-range electrostatic cutoff
> (in nm)
> rvdw =1.4 ;short-range van der Waals cutoff
> (in nm)
>
> ;Electrostatics
> coulombtype =PME ;Particle Mesh Ewald for long-range
> electrostat;ics
> pme_order =4 ;cubic interpolation
> fourierspacing =0.16 ;grid spacing for FFT
>
> ;Temperature coupling is on
> tcoupl =V-rescale ;modified Berendsen
> thermostat
> tc-grps =SYSTEM ;one coupling group
> tau_t =0.1 ;time constant, in ps
> ref_t =298 ;reference temperature, one
> for
> each ;group, in K
>
> ;Pressure coupling is on
> pcoupl =Parrinello-Rahman ;Pressure coupling on in NPT
> pcoupltype =isotropic ;uniform scaling of
> box vectors
> tau_p =2.0 ;time constant, in ps
> ref_p =1.0 ;reference
> pressure, in bar
> compressibility =4.5e-5 ;isothermal compressibility of h2O,
> 1/bar
>
> ;Periodic boundary conditions
> pbc =xyz ; 3-D PBC
>
> ;Dispersion correction
> DispCorr =EnerPres ;account for cut-off vdW
> scheme
>
> ;Velocity generation
> gen_vel =no ;Velocity generation is off
>
The problem should be with your topology. List your ITP files.
--
Dr. Vitaly V. Chaban, Department of Chemistry
University of Rochester, Rochester, New York 14627-0216
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