[gmx-users] Hessian matrix within gmx mdrun

Hello, I'm trying to do a normal modes analysis on a large crystalline system (~100,000 atoms of MgO). I expected the hessian to be (300,000x300,000), or NDIM*natoms, but by poking around in the source code a *little*, I can see that the Hessian is made only by the atom types, not by the actual at

Re: [gmx-users] Invalid order for directive atomtypes for ligands

On 6/28/18 4:19 PM, Qasim Pars wrote: Dear users, I have a protein bound to two different ligands. LIG1.itp and LIG2.itp files of both ligands include [ atomtypes ] part. I get "Invalid order for directive atomtypes" error while running energy minimization step. Do I have to combine [ atomtyp

[gmx-users] Invalid order for directive atomtypes for ligands

Dear users, I have a protein bound to two different ligands. LIG1.itp and LIG2.itp files of both ligands include [ atomtypes ] part. I get "Invalid order for directive atomtypes" error while running energy minimization step. Do I have to combine [ atomtypes ] parts of both ligands to get rid of th

Re: [gmx-users] Potential energy reported by gmx energy command

Den 2018-06-28 kl. 09:03, skrev atb files: Hello experts, I did a LJ particles simulation, where I simulated two systems, 100 particle and 400 particle. For 100 particles energy is: Energy  Average   Err.Est.   RMSD  Tot-Drift ---

Re: [gmx-users] Use different version of tpr in the same simulation... possible ?

On 6/28/18 10:17 AM, ABEL Stephane wrote: Hi there For different reason, I have to use a different version of GROMACS (GMX2016.4) to continue a simulation carried out with GROMACS v2018. Obvioulsy I obtain an error appears about the tpr "reading tpx file version 112 with version 110 prog

[gmx-users] Use different version of tpr in the same simulation... possible ?

Hi there For different reason, I have to use a different version of GROMACS (GMX2016.4) to continue a simulation carried out with GROMACS v2018. Obvioulsy I obtain an error appears about the tpr "reading tpx file version 112 with version 110 program" Is there an alternative to do what I want

[gmx-users] Umbrella sampling

Hi, I do umbrella sampling for different distances of AA along surface and i calculated error by bootstrapping method. Error is less than 0.5 kj.mol-1 in 0.8to1.7 nm far from surface, but in 0.6to0.8 nm error is about 2 kj.mol-1 . The minimum energy is about -5kj.mol-1 at 0.65 nm. All windows over

Re: [gmx-users] Fwd: Ionic liquid and CNTs

Thanks a lot ! I'm going to do it straight away ... I'll let you know the results ! Thanks ever so much ! Candy 2018-06-28 9:43 GMT+02:00 Alex : > Ah, that's a scary looking system. :) > > Indeed, there are vacuum pockets, because the system has not been brought > to correct pressure. All you hav

[gmx-users] Potential energy reported by gmx energy command

Hello experts, I did a LJ particles simulation, where I simulated two systems, 100 particle and 400 particle. For 100 particles energy is: Energy       Average   Err.Est.   RMSD  Tot-Drift --- Potenti

Re: [gmx-users] Fwd: Ionic liquid and CNTs

Ah, that's a scary looking system. :) Indeed, there are vacuum pockets, because the system has not been brought to correct pressure. All you have to do for your relaxation run is use a semiisotropic barostat (maybe Berendsen, but only for relaxation) with a realistic solvent compressibility in

Re: [gmx-users] Fwd: Ionic liquid and CNTs

Hi Alex, Thanks for your answer ... Here is the pdb file of my system : https://files.fm/u/7crt2yd5 Candy 2018-06-27 22:30 GMT+02:00 Alex : > If there is a bubble, all it could mean is that the volume simply too > large, which could be expected, given the combination of short simulation > and low