Re: [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

Hi, On Wed., 12 Jun. 2019, 07:47 Prasanth G, Research Scholar, < prasanthgha...@sssihl.edu.in> wrote: > Dear Bratin, > > Thank you for your prompt response. would using an isotropic pcoupletype > have any effect on a membrane protein simulation? > It will keep the box vectors in the same ratio,

Re: [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

Dear Bratin, Thank you for your prompt response. would using an isotropic pcoupletype have any effect on a membrane protein simulation? If we provide same ref_p values for all three axis (as in the above case)in a semiisotropic treatment, would this have the same effect as isotropic treatment? I

Re: [gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

Hi This is happening because in ... pressure coupling you mentioned semi-isotropic ...where the pressure will be uniform in x-y box vector..not the z direction... that's why your box is becoming rectangular. You can use isotropic pressure coupling for maintaining the sqare shape of the

[gmx-users] compressed pbc box at the end of simulation - membrane protein with ligand

Dear all, I am carrying out a simulation of membrane protein with a ligand. I am using DPPC [slipids (http://www.fos.su.se/~sasha/SLipids/Downloads.html)]. I had modified amber 03 ff by including the non-bonded and bonded parameters from slipids website as suggested in the tutorial by Justin (