[gmx-users] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation
niexuechuan at 126.com
Tue Apr 14 03:44:19 CEST 2015
Thanks for your suggestion. I will try for it.
Sciences: Nie Xuechuan
At 2015-04-12 04:34:18, "Thomas Piggot" <t.piggot at soton.ac.uk> wrote:
>Justin is right about the parameters being sub-optimal, for example see:
>de Vries et al. http://pubs.acs.org/doi/abs/10.1021/jp0366926
>which I think was the first mention of issues with the 'Berger' PE
>There are plenty of force fields out there for PE membranes (both
>all-atom and united-atom) which do a much better job. If you really
>really want to use Berger you can use the fudge as mentioned in this
>paper to include some repulse LJ interactions on the headgroup
>hydrogens. From some tests I did ages ago, I think you need a larger
>repulsive force than is mentioned in the paper (which uses DOPE) to get
>POPE to behave sensibly (IIRC).
>On 11/04/15 21:09, Justin Lemkul wrote:
>> On 4/11/15 8:25 AM, niexuechuan wrote:
>>> Dear all, I am new to lipid simulation. I have downloaded the pope.pdb,
>>> pope.itp, lipid.itp from Tieleman's web site
>>> (http://wcm.ucalgary.ca/tieleman/downloads). And I have made a directory
>>> named gromos53a6_lipid.ff followed Justin's tutorial
>>> Then I use pope.pdp to run a pure 340 POPE lipid MD at 310K. But I
>>> find that
>>> the box of xy dimension will shrink from 9.6nm*9.5nm to 9.0nm*8.9nm
>>> after 20
>>> ns, then it fluctuates at that value till 200ns. The box of z
>>> dimension will
>>> increase a little to hold the volume constant. This will lead to the
>>> per lipid decreased from 0.54 nm^2 to 0.47nm^2. At the same time, I
>>> the order parameter of lipid tail (Scd) is too big (above 0.3). Does
>>> any one
>>> know where the problem is?
>> This could very well be due to suboptimal parameters. Has anyone ever
>> verified that these POPE parameters produce APL and order parameters
>> in agreement with experimental values over such long time frames?
>> Lipid force fields are very sensitive and not all parameter sets are
>> created equal.
>>> When I use dppc128.pdb from Tieleman's web site to run a pure DPPC
>>> MDat 323K, the box will not shrink. And the area per lipid of DPPC is in
>>> accordance with literature, about 0.62nm^2.
>>> The water model is SPC. My mdp file is also from Justin's tutorial.
>>> is my mdp file of POPE:
>>> title= KALP15-DPPC Production MD ; Run parameters integrator= md;
>>> integrator nsteps= 100000000; 2 * 500000 = 1000 ps (1 ns) dt = 0.002; 2
>>> fs ; Output control nstxout= 0; save coordinates every 2 ps nstvout=
>>> 0; save
>>> velocities every 2 ps nstxtcout= 1000; xtc compressed trajectory
>>> output every
>>> 2 ps nstenergy= 1000; save energies every 2 ps nstlog= 1000; update
>>> log file
>>> every 2 ps ; Bond parameters continuation= yes ; Restarting after NPT
>>> constraint_algorithm = lincs; holonomic constraints constraints=
>>> ; all bonds (even heavy atom-H bonds) constrained lincs_iter=
>>> 1 ;
>>> accuracy of LINCS lincs_order= 4 ; also related to accuracy ;
>>> Neighborsearching ns_type= grid; search neighboring grid cels
>>> nstlist= 5 ;
>>> 10 fs rlist= 1.2; short-range neighborlist cutoff (in nm) rcoulomb= 1.2;
>>> short-range electrostatic cutoff (in nm) rvdw= 1.2; short-range van
>>> der Waals
>>> cutoff (in nm) ; Electrostatics coulombtype= PME; Particle Mesh Ewald
>>> long-range electrostatics pme_order= 4 ; cubic interpolation
>>> fourierspacing= 0.16; grid spacing for FFT ; Temperature coupling is on
>>> tcoupl= Nose-Hoover ; More accurate thermostat tc-grps= POPE
>>> three coupling groups - more accurate tau_t= 0.50.5;0.5 ; time
>>> constant, in ps ref_t= 310 310;323 ; reference temperature,
>>> one for
>>> each group, in K ; Pressure coupling is on pcoupl=
>>> Parrinello-Rahman ;
>>> Pressure coupling on in NPT pcoupltype= semiisotropic ; uniform
>>> scaling of
>>> x-y box vectors, independent z tau_p= 2.0 ; time constant, in ps
>>> ref_p= 1.01.0 ; reference pressure, x-y, z (in bar)
>>> compressibility =
>>> 4.5e-54.5e-5; isothermal compressibility, bar^-1 ; Periodic boundary
>>> conditions pbc = xyz; 3-D PBC ; Dispersion correction DispCorr=
>>> account for cut-off vdW scheme ; Velocity generation gen_vel= no;
>>> generation is off ; COM motion removal ; These options remove motion
>>> of the
>>> protein/bilayer relative to the solvent/ions nstcomm = 1
>>> = Linear comm-grps = POPE SOL ; Scale COM of reference coordinates
>>> (when postion restraint) ;refcoord_scaling = com
>>> And my topol file: #include "gromos53a6_lipid.ff/forcefield.itp"
>>> ; Include water topology #include "gromos53a6_lipid.ff/spc.itp"
>>> ; System specifications [ system ] 340-Lipid POPE and CNP [ molecules
>>> ] ;
>>> molecule name nr. POPE 340 SOL 6729 Thanks in advance,
>>> Nie Xuechuan Shanghai Institute of Applied Physics, Chinese Academy of
>Dr Thomas Piggot
>University of Southampton, UK.
>Gromacs Users mailing list
>* Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>* For (un)subscribe requests visit
>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.
More information about the gromacs.org_gmx-users