[gmx-users] Restraints Riddle/Pull Puzzle

Okay, so... I have a U shaped protein and the diameter of the U is larger than half the shortest box vector. And it is already a huge box. I want to prevent the U from straightening out. My attempts at distance restraints fail because the shortest distance between the ends of the U is across the

Re: [gmx-users] trjconv - two chains are separated

For "-pbc nojump" to work, you need to make sure they are together (as you want) in the first frame of your input trajectory. The most reliable way to do this is by centering the trajectory on a residue at the interface between the two chains (using a custom index group). I've also heard some peo

[gmx-users] What's the practical effect of 'continuation = yes/no'?

What exactly does 'continuation = yes' do? My understanding thus far is that it will move particles in the first step (using the input velocities) before applying the constraints (LINCS bond lengths etc.). When continuing a simulation with 'continuation=no' you would apply constraints twice in a r

Re: [gmx-users] Unexpected trjconv -nojump behaviour

e any trouble. I can only assume I'm making some invalid assumptions about how the commands work. -Trayder On Tue, Mar 31, 2015 at 7:15 PM, Tsjerk Wassenaar wrote: > Hi Trayder, > > The first frames did not have the same position/orientation and/or the same > box. > > Cheers

[gmx-users] Unexpected trjconv -nojump behaviour

Hi, I'm struggling with pbc nojump for a particular starting structure and don't understand why. The system starts with a broken conformation so I've concatenated it onto a whole structure such that the whole structure is the first frame: trjcat -f whole.xtc md1-1.xtc -cat -o test.xtc I then look

Re: [gmx-users] Using Gpus on multiple nodes. (Feature #1591)

Try: mpirun -npernode 2 -Trayder On Wed, Oct 15, 2014 at 8:42 AM, Siva Dasetty wrote: > Thank you Mark for the reply, > > We use pbs for submitting jobs on our cluster and this is how I request the > nodes and processors > > #PBS -l > select=2:ncpus=8:mem=8gb:mpiprocs=8:ngpus=2:gpu_model=k20:in

Re: [gmx-users] rhombic dodecahedron construction

(ux vy wz uy uz vx vz wx wy). Finally, note that the > box (any box) is written in its triclinic representation, which is easiest > to handle mathematically. > > Hope it helps, > > Tsjerk > > > > On Fri, May 23, 2014 at 4:42 AM, Trayder Thomas > wrote: > &g

[gmx-users] rhombic dodecahedron construction

Hi, I'm trying to figure out how to construct a rhombic dodecahedron for a membrane system. The manual (Section 3.2.1) states: "There are two different orientations of a rhombic dodecahedron that satisfy equations 3.1, 3.2 and 3.3. The program editconf produces the orientation which has a square

Re: [gmx-users] Detection of Internal water along MD trajectory

If you can think of a sensible way to define your area of interest, a simple VMD script can count waters: [atomselect "name \"O.*\" and resname and same residue as " frame ] num e.g. To count the number of water molecules within 5A of residues 1-5: [atomselect 0 "name \"O.*\" and resname SOL and

Re: [gmx-users] At what point is the random seed generated?

at 8:51 AM, David van der Spoel > wrote: > > > On 2014-01-28 08:37, Trayder Thomas wrote: > > > >> Hi, > >> When using 'gen-seed = -1' at what point is the random seed assigned? > >> > >> e.g. Does it use the process ID of grompp and em

[gmx-users] At what point is the random seed generated?

Hi, When using 'gen-seed = -1' at what point is the random seed assigned? e.g. Does it use the process ID of grompp and embed the seed number in the tpr file, or does it use the process ID of mdrun? I ask because I have 50 identical simulations started from the same tpr file :( Thanks, -Trayder