Hi gmx-users, <br>I added simulation box by *editconf below mentioned to POPC system downloaded from Tieleman's website, I don't want to add water <br>1) *editconf -f popc.gro -o popc_box.gro -box 6 6 9 -c this one I followed based on gmx-archives.<br>
2) Then in 2ndcase I used same command but 8 8 8(cubic) instead of 1st case numerical values .<br> After this I did *EM system is fine for both cases when visualise in VMD. when I do *PR I am getting problem in second way of using *editconf rather than first way. I got fine structure in first case (without distortions in water and membrane). In 2nd case displacement of water ( totally there is no cubic structure at all ). Now my doubt is shall I use 1 case output file for my further simulations? or any mistake in my command or pr.mdp file ? while I am using it runs fine. Is it mandatory to add cubic box?<br>
<br>Pls help me I am posting my pr.mdp file(similar parameter for both cases)<br><br>title = popc restrained<br>define = -DPOSRES_LIPID<br>constraints = all-bonds<br>integrator = md<br>
dt = 0.002 ; ps !<br>nsteps = 10000 ; total 50 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 = 1.0 1.0 1.0 1.0 1.0 1.0<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>Thanks in advance. <br>