Re: [gmx-users] Re: charge group in topology file

[EMAIL PROTECTED] wrote: Hi, All I am running gromacs for simulation of 5 peptides. I have a problem with the topology file in which the charge on each and every charge group is not coming whole but in some of them it is in fraction which is not correct. I have used G43a1 as well as OPLS but i a

Re: [gmx-users] Diffusion Cofficient of POPC

minnale wrote: Hi all, I have read the literature about Diffusion cofficient(Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion, Vol-125, page-204703, Journal-THE JOURNAL OF CHEMICAL PHYSICS) then I have given co

[gmx-users] Re: charge group in topology file

Hi, All I am running gromacs for simulation of 5 peptides. I have a problem with the topology file in which the charge on each and every charge group is not coming whole but in some of them it is in fraction which is not correct. I have used G43a1 as well as OPLS but i am getting the same problem

Re: [gmx-users] Diffusion Cofficient of POPC

Dear Minnale, As far as i know, at least 100ns simulation should be performed in order to obtain the correct diffusion coefficient for lipids. I think, if you performed 5 ns it is too short. Hope this helps. balazs minnale wrote: Hi all, I have read the literature about Diffusion coffi

[gmx-users] Diffusion Cofficient of POPC

Hi all, I have read the literature about Diffusion cofficient(Dynamics in atomistic simulations of phospholipid membranes: Nuclear magnetic resonance relaxation rates and lateral diffusion, Vol-125, page-204703, Journal-THE JOURNAL OF CHEMICAL PHYSICS) then I have given command like thi

Re: [gmx-users] help

[EMAIL PROTECTED] wrote: Hi, I am trying to simulate a protein with a DPC micelle. Part of pdb files is: CRYST10.0000.0000.000 90.00 90.00 90.00 P 1 1 ATOM 1 N DPC M 1 -16.481 21.283 -0.739 1.00 0.00 MICE ATOM 2 C14 DPC M 1 -15.620 2

[gmx-users] help

Hi, I am trying to simulate a protein with a DPC micelle. Part of pdb files is: CRYST1    0.000    0.000    0.000  90.00  90.00  90.00 P 1   1 ATOM  1  N   DPC M   1 -16.481  21.283  -0.739  1.00  0.00  MICE ATOM  2  C14 DPC M   1 -15.620  20.082  -1.136  1.00  0.00

[gmx-users] cvs version and position restraints...

Hi everyone, I have a small DNA duplex in a dodecahedron box. Amber forcefield. Spce water. I have position restraints defined for the whole duplex in my topology. I'm running exactly the same input script on 2, 4 and on 12 cpus. The one with 12 produces a trajectory in which it is quite clear

[gmx-users] Using user-tables for simulations in vacuum

Hello users, I am trying to do a simulation of a polymer chain (which is simply a bead of unified methane molecules) in vacuum using user-defined tables. The interactions are Weeks-Chandler-Andersen instead of Lennard-Jones. However, when I run the simulations, mdrun gives me a segmentation fault.

[gmx-users] Simulation of silicon oxide surfaces

Hello, I want to set up a silicon oxide surface with varying -OH surface group for my simulation. Does anybody know a tool that could do that or maybe even has a topology I could start on and alter manually? Thanks for any sugesstions, Michael -- http://www.defux.de _

Re: [gmx-users] Microcanonical MD with PBC

Lee-Ping Wang wrote: Hi everyone, I've been trying to get a microcanonical (energy conserving, NVE) MD run with periodic boundary conditions. I'm using the provided box of 216 water molecules and the SPC force field (flexible). When I turn PBC off, the energy RMSD is <0.01kJ/mol with a 0.1fs t

Re: [gmx-users] Calculating electric field vector at snapshots

Aaron Fafarman wrote: Thank you for considering my proposed scheme for calculating the electric field vector at a single site at every snapshot of an MD trajectory. As discussed previously on this list, I have attempted to use a virtual site with no mass and with an infinitesimal charge, construc