[gmx-users] Handling Periodic Boundary Conditions

Hi all, I'm having trouble with visualisation of my system after the MD production run. I have tried the periodic boundary conditions workflow suggested on the gromacs website, although I'm having no luck. I have used the following command to try and obtain a visualisation state that I can

[gmx-users] Umbrella Sampling

Hello; i'm using umbrella sampling and i have some basic questions about it, i will appreciate you if you help me; 1. for example i've got 2000 conf.gro and i want to choose 38 of them. i dont know how choose them eficiently???(The conformations are scanned every 0.1 ps in order to save them

[gmx-users] Umbrella Sampling

Hello; i'm using umbrella sampling and i have some basic questions about it, i will appreciate you if you help me; 1. for example i've got 2000 conf.gro and i want to choose 38 of them. i dont know how choose them eficiently???(The conformations are scanned every 0.1 ps in order to save them

[gmx-users] Umbrella Sampling

Hello i'm trying to do umbrella sampling and this is md_umbrella.mdp; DEFINE = -DPOSRES integrator = md dt = 0.001 nsteps = 4000 nstxout = 0 nstvout = 0 nstfout = 0

[gmx-users] Umbrella Sampling

Hello i'm trying to do umbrella sampling and this is part of md_umbrella.mdp; DEFINE = -DPOSRES integrator = md dt = 0.001 nsteps = 4000 nstxout = 0 nstvout = 0 nstfout

Re: [gmx-users] Two questions: LAMMPS to gromacs, Test particle insertion

You can try InterMol for converting between LAMMPS and GROMACS (and a few other engines): https://github.com/shirtsgroup/InterMol > On Nov 21, 2017, at 9:26 AM, Arun Srikanth wrote: > > Hello all, > > I have two questions. >

Re: [gmx-users] overlapped parameters

On 11/21/17 4:48 AM, Albert wrote: Hello, I have set my topol.top file as following: ; Include forcefield parameters #include "charmm36-jul2017.ff/forcefield.itp" #include "input/unk.prm" #include "input/unk.itp" Then I run grompp command line. I obtained the following warnings: WARNING 1

[gmx-users] Two questions: LAMMPS to gromacs, Test particle insertion

Hello all, I have two questions. 1. Is there a tool to convert LAMMPS data file to gromacs topology file. I am using GAFF forcefield. Test particle insertion: In the manual it is mentioned that "This trajectory should not contain the molecule to be inserted." If I want to estimate excess

[gmx-users] Performance test

Dear users, I'm doing a performance analysis following this link http://manual.gromacs.org/documentation/5.1/user-guide/mdrun-performance.html and wanted to ask: Is there a "standard" procedure to test performance in gromacs (on single nodes, one multi-processor CPU)? Following there are some

[gmx-users] gmx angle memory consumption

Hi, I want to calculate dihedral angles for long trajectories at high sampling rates using gmx angle as follows: gmx angle -f traj.xtc -n dih_indices.ndx -ov dih.xvg -type dihedral -all After some time, it completely fills my RAM without having written anything to the output file. As the

Re: [gmx-users] Inconsistency in units of virtual sites?

Ah, thank you very much, I completely missed that table.. And it is also a 'logical' unit, now I have taken a better look at equation 4.139 2017-11-21 11:23 GMT+01:00 Peter Kroon : > Hoi Douwe, > > > according to the manual the units are indeed inconsistent (but > documented,

[gmx-users] equal systems

Hello, Which physical quantities must be equal in simulation results of two systems in order to say they are physically equal (or which quantities are enough to check)? Best, -- Gromacs Users mailing list * Please search the archive at

Re: [gmx-users] Inconsistency in units of virtual sites?

Hoi Douwe, according to the manual the units are indeed inconsistent (but documented, and therefore ok). See table 5.5 of the manual. For 3out the unit of c is in nm^-1. Peter On 21-11-17 10:15, Douwe Pollmann wrote: > Thanks Justin for the reply. > > I'm sorry for the inconvenience, I put

[gmx-users] overlapped parameters

Hello, I have set my topol.top file as following: ; Include forcefield parameters #include "charmm36-jul2017.ff/forcefield.itp" #include "input/unk.prm" #include "input/unk.itp" Then I run grompp command line. I obtained the following warnings: WARNING 1 [file unk.prm, line 22]:   Overriding

Re: [gmx-users] Inconsistency in units of virtual sites?

Thanks Justin for the reply. I'm sorry for the inconvenience, I put 1/3 in stead of 0.333 in this example for clarity, but apparently it wasn't clear at all.. Below a part of the real .itp file is shown: ; The virtual sites for the side chain beads [ virtual_sites3 ] ;Site from

Re: [gmx-users] Applying an electric field on lipids

So, you have a charged protein under a high electric field, moving and bumping into an unrestrained lipid bilayer. Maybe use position restraints, those are well documented in the Gromacs manual. Alex On 11/20/2017 11:23 PM, Sithara Perera wrote: The .mdp file parameter for electric field is