Re: [gmx-users] Dangling phospholipids

. Lemkul escribió: Dr. Ramón Garduño-Juárez wrote: Dear All, First of all I want to tank Justin Lemkul and Thomas Piggot for their useful comments that helped me to resolve my previous questions regarding the construction of a lipid membrane. Now I would like to post this question to this

[gmx-users] Problems with a three domain protein in a membrane

Dear all, Dear Justin, We have been working on setting up an MD experiment in which our system is made of three separate domains of a protein embedded in a DMPC bilayer surrounded by water. We have generated a PDB file in which our three domains are labeled as A, B and C (in the column corre

[gmx-users] Splitted DMPC bilayer

Dear all, Dear Justin, This time I want to ask the gurus about this problem I encountered in the Equilibration step of my system made of 3 individual (small) protein chains in a solvated DMPC bilayer, no ions present since the protein system is neutral... Following the tutorial I started wit

Re: [gmx-users] Splitted DMPC bilayer

mkul escribió: Dr. Ramón Garduño-Juárez wrote: Dear all, Dear Justin, This time I want to ask the gurus about this problem I encountered in the Equilibration step of my system made of 3 individual (small) protein chains in a solvated DMPC bilayer, no ions present since the protein system is ne

Re: [gmx-users] Splitted DMPC bilayer

know that there was no "error", which I meant is that I was surprised by the outcome... May be GROMACS is as fast as it is claimed... Cheers, Ramon El 04/04/2011 05:27 p.m., Justin A. Lemkul escribió: Dr. Ramón Garduño-Juárez wrote: Justin, Thank you for your comments after fin

[gmx-users] If the system net charge is zero, do I need to add ions?

Hi GROMACS users, I've two questions. My simulation box contains a DMPC lipid bilayer, water molecules, intramembrane protein and a ligand protein. The net charge of the system is zero. Is it necessary to add ions to this system? The intramembrane protein (made of two chains) has a net charge

[gmx-users] How to create an rtp file for a lipid?

Dear All: I am trying to build a lipid bilayer made of DMPC (Dimyristoylphosphatidylcholine) surrounding a putative membrane channel. Everything goes well until I come across with the use of pdb2gmx and further on to the use of gromp, where I realized that I need to add some information about

[gmx-users] grompp charge group radii larger than rlist

Dear All: I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have reached step three, when I try to generate a trp file for DPPC only by means of : grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr I get the following warning: WARNING 1 [file minim.mdp]: The

[gmx-users] Dangling phospholipids

Dear All, First of all I want to tank Justin Lemkul and Thomas Piggot for their useful comments that helped me to resolve my previous questions regarding the construction of a lipid membrane. Now I would like to post this question to this forum. I got through placing a putative ion channel i