Re: [gmx-users] Re: question about freeze

I think your RMSD of 0.000539742 is quite a small value, which can be, at least theoretically, caused by the accumulation of errors. Can you simulate your protein for a longer time to show that RMSD is indeed significant? On Sat, Jul 28, 2012 at 1:01 AM,

[gmx-users] Re: system blowing up

Thanks for your reply. I'm following the protocol of Diagnosing an unstable system. Corresponding the first step I changed th nstxout to 1 for 3 times. The first and second time I got error the same as before ( some interactions seem to be assigned multiple times ) and it the warning as

[gmx-users] Re: question about freeze

I want to do a minimization and a md run with my protein. But I only want the hydrogen atoms to be minimized but not the rest of the protein. I use the freezegrps = Protein-H freezedim = Y Y Y option in my mdp files to make sure that they don't change. During the minimization steps

[gmx-users] Re: Error in Membrane simulations with POPC bilayer (

I have the following Notes during NPT equilibration. NOTE 1 [file pr_NPT.mdp]: nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting nstcomm to nstcalcenergy NOTE 2 [file pr_NPT.mdp]: leapfrog does not yet support Nose-Hoover chains, nhchainlength reset to 1 What do

[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

I am trying to change all lipid acyl tails to a trans orientation, and thought that restraining all tail dihedrals to 180 should work quickest. I have also tried smaller angles (120, 100) and the effect is the same, leaflets drifting apart. In fact, the 180 restraint does work fine in vacuo

[gmx-users] Re: Calculation of instantaneous dipole moment

Dear All I want to obtain the instantaneous dipole moment as an output for the OH bond in the pure water molecule simulation. Given the conditions that most of the water models have fixed coordinates and charges during the course of simulation how can I get the same.Is there any

[gmx-users] Re: bilayers move apart by nanometers upon implementing dihedral restraints on lipid tails

I am trying to implement dihedral restraints for lipids in a bilayer using what is suggested here: http://www.gromacs.org/Documentation/How-tos/Dihedral_Restraints However, although the dihedral angles seem to be restrained fine, the leaflets move apart by 10s of nanometers along +z over a

Re: [gmx-users] COM RDF

Dear GROMACS people - I am calculating radial distribution function between the centers of mass of two large particles in a periodic box. My command is -- g_rdf_455 -n 2drops.ndx -rdf mol_com -s topol.tpr -f conf.gro My index file contains two groups of atoms standing for the first and

Re: [gmx-users] center an atomic group

On 6/21/12 3:20 PM, Dr. Vitaly V. G. Chaban wrote: Dear All - I have a macromolecule surrounded by multiple layers of water in my box. For visualization purposes, I would like to center the macromolecule in the box (PDB file), so that its geometrical center coincides with the geometrical

[gmx-users] Re: bond autocorrelation function

Hello Does gmx provide any script to calculate autocorrelation function for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ? Thanks a lot for the information! Assuming that you mean the aucorrelation function (ACF) of the bond length fluctuations around its equilibrium

[gmx-users] Re: bond autocorrelation function

Does gmx provide any script to calculate autocorrelation function for a defined bond (not hydrogen bond autocorrelation function,g_hbond) ? Thanks a lot for the information! Assuming that you mean the aucorrelation function (ACF) of the bond length fluctuations around its equilibrium