<div dir="ltr"><div class="gmail_quote"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Thank you very much to Xavier for your valuable suggestion<br>
>>> > Hi Users,<br>
>> >> > I have extended the lipid bilayer(popc) from default<br>
>> >> popc128a.pdb to<br>
>> >> > 200 popc molecules with suffcient water by using genbox.<br>
>> >> > genbox -cs 128a.pdb -o out.gro -p 128a.top -box 9.2 9.2 6.9,<br>
>> >> to the<br>
>> >> > out.gro(contain 200 popc) minimisation ran fine later swtich over<br>
>> >> to *PR<br>
>> >> > with fc-1000 on P8,C51,C53 of popc and saw output_pr.gro in VMD<br>
>> >> water has<br>
>> >> > weird strcuture(up side downs but popc structure is quite fine).<br>
>> >> > So I have reduced the pbc box size to 9 9 6.7 with *editconf<br>
>> >> later I ran<br>
>> >> > minimsation and *PR, "now water" and POPC structures are "fine"<br>
>> but I<br>
>> >> > observed "unequal water".<br>
>> >><br>
>> >><br>
>> >><br>
>> >> What do you mean with "unequal water"?<br>
>> >><br>
>> >> Thanks for the response unequal water means ' when I noticed the<br>
>> >> intial 200popc.gro use VMD water molecules present bothsides almost same<br>
>> >> towards corners of the simulation box and centre of the above and below<br>
>> >> popc heads but after *PR one side of the leaflet bilayer corners have<br>
>> >> very less water (say 20 water molecules earlier 80 water molecules)<br>
>> >> looks at corners doesnt have water seems. I hope you understood my<br>
>> problem,<br>
>> >><br>
>> ><br>
>> > Probably your system isn't perfectly centered within the box and you are<br>
>> >seeing "diffusion" from PBC.<br>
>> It is however not totally clear (to me) what is the problem. If it is a<br>
>> change of water density in a particular area of the simulation box, it<br>
>> could<br>
>> well be that the water distribution was not so "ideal" in your starting<br>
>> configuration.<br>
>><br>
> Justin suggestion "run a bit longer" is good. especially that you have not<br>
>> given us much information on that!<br>
>><br>
><br>
> Thanks for the replies, I have run only 500ps *PR step and attaching<br>
> pr.mdp file<br>
> title = popc restrained<br>
> define = -DPOSRES<br>
> constraints = all-bonds<br>
> integrator = md<br>
> dt = 0.002 ; ps !<br>
> nsteps = 250000 ; total 500 ps.<br>
> nstcomm = 1<br>
> nstxout = 50<br>
> nstvout = 1000<br>
> nstfout = 0<br>
> nstlog = 10<br>
> nstenergy = 10<br>
> nstlist = 10<br>
> ns_type = grid<br>
> rlist = 0.9<br>
> coulombtype = PME<br>
> rcoulomb = 0.9<br>
> rvdw = 1.4<br>
> pbc = xyz<br>
> ; Berendsen temperature coupling is on in two groups<br>
> Tcoupl = Berendsen<br>
> tc-grps = POPC SOL<br>
> tau_t = 0.1 0.1<br>
> ref_t = 323 323<br>
> ; Anisotropic pressure coupling is now on<br>
> Pcoupl = berendsen<br>
> pcoupltype = anisotropic<br>
> tau_p = 2.0 2.0 2.0 0 0 0<br>
> compressibility = 4.5e-5 4.5e-5 4.5e-5 0 0 0<br>
> ref_p = 1.0 1.0 1.0 0 0 0<br>
> ; Energy monitoring<br>
> energygrps = POPC SOL<br>
> ; Generate velocites is on at 300 K.<br>
> gen_vel = yes<br>
> gen_temp = 323.0<br>
> gen_seed = 173529<br>
><br>
><br>
> Could you suggest me if any wrong in this pr.mdp file, may be this is<br>
> trivial query<br>
> As both of you said simulate bit longer, if yes will it cause equal<br>
> distribution of water?<br>
> Thanks in advance.<br>
<br>
Well nothing obviously wrong in the mdp file.<br>
It may be time to let the lipids free to move ...<br>
<br></blockquote></div><br></div>