<div dir="ltr"><br><br><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;">>> > 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" 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 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 could<br>
well be that the water distribution was not so "ideal" in your starting<br>
configuration. <br></blockquote><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Justin suggestion "run a bit longer" is good. especially that you have not<br>
given us much information on that!<br></blockquote></div> <br> Thanks for the replies, I have run only 500ps *PR step and attaching 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>Could you suggest me if any wrong in this pr.mdp file, may be this is trivial query <br>
As both of you said simulate bit longer, if yes will it cause equal distribution of water?<br>Thanks in advance. <br></div>