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

[niexuechuan]

Dear Thomas;
         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 
>parameters.
>
>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).
>
>Cheers
>
>Tom
>
>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
>>> (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
>>>
>>
>
>-- 
>Dr Thomas Piggot
>University of Southampton, UK.
>
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