[gmx-users] Re: Unsteady Density
Justin A. Lemkul
jalemkul at vt.edu
Mon May 2 23:02:15 CEST 2011
Fabian Casteblanco wrote:
> Thanks Justin.
>
> I'm currently running the MD run separately so that the average value
> won't be affected by the unequilibrated values at the beginning of the
> NPT run where the density started in the 400s and ran up to the ~high
> 700s. I had done this before when I had nstlist at 5 but I did run
> NPT for a lot shorter time last time so Im hoping this time it will be
> better since last time it was still off (0.781 g/cm3 to 0.791 g.cm3).
> I will also change the compressibility. Do you think increasing the
> rlist, rcoulomb, rvdw value to about 1.6, 1.8 nm might also work a bit
> better?
>
No, in fact it will probably make it worse. Use the values prescribed by the
force field.
-Justin
> Thanks again.
>
> On Mon, May 2, 2011 at 2:16 PM, Fabian Casteblanco
> <fabian.casteblanco at gmail.com> wrote:
>> Hello,
>>
>> 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
>>
>>
>>
>> --
>> Best regards,
>>
>> Fabian F. Casteblanco
>> Rutgers University --
>> Chemical Engineering PhD Student
>> C: +908 917 0723
>> E: fabian.casteblanco at gmail.com
>>
>
>
>
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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