<div dir="ltr">Hi Users, <br> I have extended the lipid bilayer(popc) from default popc128a.pdb to 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, to the out.gro(contain 200 popc) minimisation ran fine later swtich over to *PR with fc-1000 on P8,C51,C53 of popc and saw output_pr.gro in VMD water has 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 later I ran minimsation and *PR, "now water" and POPC structures are "fine" but I observed "unequal water".<br><br>Could you tell me, did I miss something to use<br>
Any suggestions would be appreciated<br>Thanks in advance<br> <br> <br></div>