[gmx-users] POPE lipid from Tieleman's web site, the box of xy dimension will shrink during the simulation

[niexuechuan]

Dear Justin;
         Thanks for your reply!  Maybe I will use other kind of lipid or force field instead.
 Sciences: Nie Xuechuan









At 2015-04-12 04:09:24, "Justin Lemkul" <jalemkul at vt.edu> 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
>> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html).
>> 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 area
>> per lipid decreased from 0.54 nm^2 to 0.47nm^2.   At the same time, I find
>> 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.
>
>-Justin
>
>> When I use dppc128.pdb from Tieleman's web site  to run a pure DPPC lipid
>> 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. Followed
>> is my mdp file of POPE:
>>
>>
>> title= KALP15-DPPC Production MD ; Run parameters integrator= md; leap-frog
>> 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
>> ; 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 for
>> 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 SOL;SOL_CL;
>> 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= EnerPres;
>> account for cut-off vdW scheme ; Velocity generation gen_vel= no; Velocity
>> generation is off ; COM motion removal ; These options remove motion of the
>> protein/bilayer relative to the solvent/ions nstcomm         = 1 comm-mode
>> = 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
>> "pope.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
>> Sciences
>>
>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
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