Re: [gmx-users] No convergence with g_nmeig

Dear gromacs users, I still have the same problem with the vector convergence. There is a link with the size of my protein (18 081 atoms) ? I tried with a small molecule composed with 826 atoms and it seems to work. Any idea, please. Best Esra Hi,

[gmx-users] H-REMD in umbrella sampling

Hi, Is Hamiltonian REMD possible with umbrella sampling in pure gromacs 5.1 without plumed patch ? It should be according to gromacs 5 paper and manual but no details are provided of how to use it. If yes, does anyone successfully applied it and could share sample mdp options used to exchange

Re: [gmx-users] cannot open traj.xtc

On 11/20/15 2:10 AM, surbhi mahajan wrote: Thankyou sir, After using g_order -s md_0_1.tpr -f md_0_1.tpr.trr -n sn1.ndx -d z -od deuter_sn1.xvg the file order.xvg is created but still my file does not give any information about the system whether it is in gel phase or liquid phase. The

[gmx-users] inertia tensor

Dear Gromacs users, I wonder whether it is possible to calculate the inertia tensor for the molecules? Thank you in advance for the answer Sten Sarman -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! *

[gmx-users] Dumping centers of mass of molecules during MD simulation

Dear Gromacs User, Instead of dumping all atoms of a specific type of molecules, I would like to dump centers of mass (COM) of the molecules during MD simulations in Gromacs to reduce trajectory storage. I know g_traj can be used to dump COM of molecules from trajectory files. But, in that

Re: [gmx-users] Gromacs 5.1 and 5.1.1 crash in REMD

Hi, Yes, that's a real bug. I'm not yet sure what to do about it, but I'll continue discussion at http://redmine.gromacs.org/issues/1848 Mark On Thu, Nov 19, 2015 at 8:06 PM Krzysztof Kuczera wrote: > Dear Justin and Mark > > Thanks for your helpful suggestions. > Yes, my

Re: [gmx-users] Dumping centers of mass of molecules during MD simulation

On 11/20/15 2:53 PM, S.M. Golam Mortuza wrote: Dear Gromacs User, Instead of dumping all atoms of a specific type of molecules, I would like to dump centers of mass (COM) of the molecules during MD simulations in Gromacs to reduce trajectory storage. I know g_traj can be used to dump COM of

Re: [gmx-users] Center of mass removal for a trajectory which is already created

To whom may have similar problem, that is how I solved it: First of all, Gromacs by default uses center of mass removal (at least in versions I use), but that is for 'whole system'. In my case I have a two-component system and I am interested in collecting density for one of the components. So,