Re: [gmx-users] how to make molecular model with both ion channel and lipid bilayer?

Charmm-gui.org could help you. Bests, Hadi On Tue, Aug 15, 2017 at 07:55 PM, "Li, Tong" wrote: Dear all, I am trying to make a model of ion channel with cell membrane. Is there a specific software to make this? I mean just the coordination file. VMD can generate the membrane automatically, I

[gmx-users] bend angles of a kink motif

Dear Users Can we calculate the bend angle of a kink motif in an alpha helix from a .xtc file? Thanks a lot. H.A -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] cpu gpu performance

Dear Users, I'm simulating a membrane protein system with approximately 185000 atoms with an Intel Corei7 cpu. I have two questions: 1. Performance of my simulations is about 1.8ns/day. Is this performance normal for such a system? Or my simulations are suffering from lack of performance? 2. when

[gmx-users] -vsite hydrogen

Dear Users, I am simulating a membrane protein with charmm ff with a 2fs time step. How the results will be affected if I use a 5fs time step by using -vsite hydrogen option in pdb2gmx? Do my results loose their accuracy if I use this option? Best wishes, H.A -- Gromacs Users mailing list *

[gmx-users] POPC with CHARMM

Dear Users, I want to simulate POPC membrane with CHARMM ff using GROMACS 4.6.5. but in CHARMM ff directory, there is no popc itp file. How can I proceed? Best, H.A -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] potassium ion in GROMOS

Dear users, How can we define potassium ion in GROMOS ions.itp file? Best, H.A -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For

[gmx-users] Electrostatic energy between two groups of atoms

Dear users, Can we calculate electrostatic energy between two groups of atoms in GROMACS? Best wishes, H.A -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] distance tracking

Dear GROMACS users, Is it possible to track H-bonding or distance between two certain atoms in GROMACS? Best wishes, Hadi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read

[gmx-users] Atom was not found

Dear Users, I want to simulate a protein by GROMACS. When I use pdb2gmx command, topology and other files are produced from my pdb file. But when I define a box for my protein by editconf before pdb2gmx, I face with this fatal error: Atom OXT in residue VAL 226 was not found in rtp entry VAL

[gmx-users] Too many LINCS warnings

Dear all, In one of my simulations when I use the command mdrun -v -deffnm nvt I face with this fatal error: Too many LINCS warnings (1056) If you know what you are doing you can adjust the lincs warning threshold in your mdp file or set the environment variable GMX_MAXCONSTRWARN to -1, but

[gmx-users] g_membed itp file

Dear GROMACS users, I'm a new GROMACS user and I would like to apologize for my basic question. I want to use g_membed to insert protein in membrane according to Wolf's paper manual. I have the pdb, mdp and top files in my directory, but when I enter the command grompp -f sample.mdp -c

[gmx-users] g_membed itp file

Dear GROMACS users, I'm a new GROMACS user and I would like to apologize for my basic question. I want to use g_membed to insert protein in membrane according to Wolf's paper manual. I have the pdb, mdp and top files in my directory, but when I enter the command grompp -f sample.mdp -c merged.gro