[gmx-users] How to calculate the MSD of center of mass of molecules

Hello everyone, In my simulation, I want to calculate the MSD of COM of some molecules using *gmx msd* command. >From the Gromacs manual, *For molecules consisting of more than one atom, ri can be taken as the center of mass positions of the molecules. In that case, you should use an index file

[gmx-users] Area per lipid through the time lipid membranes and mixed membranes

Hello gromacs user: I obtained the average area per lipid for dppc and dppe membrane, also for mixed membranes of dppc/dppe/embedded molecule. But i want to obtain the diagram of the area per lipid through the time, the course of my simulation for my dppc, dppe membranes and mixed membranes

Re: [gmx-users] Box size problem

On 3/15/17 3:09 PM, Davit Hakobyan wrote: Dear All, I try to run a simulation with protein-membrane system in charmm36 ff with Gromacs5.0.4 and the simulation runs without complain.The problem is in the unit cell size which seems to grow during a short 500 ps simulation from ~15 to ~28 nm in

Re: [gmx-users] Problem with combining the .edr files

Thanks Mark :-) Problem solved. On Wed, Mar 15, 2017 at 1:10 PM, Mark Abraham wrote: > Hi, > > Judging from your start times, you're concatenating apples with oranges :-) > In this case, probably NVT equilibration with NPT production, or similar. > Arguably,

[gmx-users] Lipid head movement normal to monolayer.

Dear all, I want to calculate how much my lipid heads emerse into water in a monolayer after simulation. I want to compare the movement of the lipids from the intial conformation to the final conformation. Is there a way to calculate such movement using GROMACS? Merril. -- Gromacs Users mailing

Re: [gmx-users] Makeing movies using VMD

Hi have look to viewchange rendering and make movie options in vmd: http://www.dxulab.com/wiki/vmdviewchangerenderingtutorial On 15/03/2017 18:16, Mark Abraham wrote: Hi, I suggest you have a look at the VMD website for their documentation. THere's very likely something for this. Mark On

Re: [gmx-users] Problem with combining the .edr files

Hi, Judging from your start times, you're concatenating apples with oranges :-) In this case, probably NVT equilibration with NPT production, or similar. Arguably, concatenating the trr files in that case is also conceptually wrong, even if the file format is not robust enough to hint that you're

[gmx-users] Box size problem

Dear All, I try to run a simulation with protein-membrane system in charmm36 ff with Gromacs5.0.4 and the simulation runs without complain.The problem is in the unit cell size which seems to grow during a short 500 ps simulation from ~15 to ~28 nm in Z direction although the system atoms

[gmx-users] Problem with combining the .edr files

Dear Gromacs users, I did a simulation in parts using -noappend command, so I have a few .trr and .edr files which I wish to merge. I have difficulty with that and I could not find any related post on that except this one: http://comments.gmane.org/gmane.science.biology.gromacs.user/68806 Using

Re: [gmx-users] EM did not converge crashing drude system

On 3/15/17 1:19 PM, Dayhoff, Guy wrote: I have a drude system that I have minimized, and equilibrated through nvt and npt ensembles using position restraints (all with scf). As I perform the production runs i’m facing random crashes that seem to be related to EM did not converge messages. This

[gmx-users] EM did not converge crashing drude system

I have a drude system that I have minimized, and equilibrated through nvt and npt ensembles using position restraints (all with scf). As I perform the production runs i’m facing random crashes that seem to be related to EM did not converge messages. This has happened anywhere from tens of

Re: [gmx-users] Makeing movies using VMD

Hi, I suggest you have a look at the VMD website for their documentation. THere's very likely something for this. Mark On Wed, Mar 15, 2017 at 6:14 PM Poncho Arvayo Zatarain < poncho_8...@hotmail.com> wrote: > > > Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1. > I

[gmx-users] Makeing movies using VMD

Hello gromacs user: I want to do a movie of my simulation using vmd 1.9.1. I finished my simulation and i have my tpr, xtc file, etc. How can i do the movie using vmd and algo save it and attach it for paste it in a powerpoint? I only can watch the trajectory in vmd, vut not save it and put

Re: [gmx-users] Computational electrophysiology, implicit solvent and coarse-grained system: atom/molecule definitions?

Hi, > On 14 Mar 2017, at 11:18, Vries, de, H.W. > wrote: > > Dear all, > > I am currently trying to run the computational electrophysiology scheme on > an implicit solvent, coarse-grained system by introducing a little > workaround: > > In the manual, it is

Re: [gmx-users] Gromacs installation on GPU

Hi, The more simple way to cater for all possibilities is to configure with GPU support the first time. mdrun observes whether there are actually GPUs at run time and executes accordingly. But as Justin says, this requires that you install CUDA when you might not use it, which is usually more

Re: [gmx-users] Gromacs installation on GPU

On 3/15/17 8:43 AM, Andrew Bostick wrote: Dear Gromacs users, I had installed gromacs using following commands: tar xvf cmake-3.6.1.tar.gz tar xvzf gromacs-5.1.3.tar.gz cd ../cmake-3.6.1. ./configure make make install cd ../gromacs-5.1.3 mkdir build cd build cmake ..

Re: [gmx-users] Distance restraints on two TYR OH groups so that they are together

On 3/15/17 6:28 AM, Vytautas Rakeviius wrote: Hello, I try to add distance restraints on two TYR OH groups so that they are together in the end like this: [ distance_restraints ] 195 281 1 1 1 0.2 0.22 0.24 1000 But it does not work at least over time frame I tested, they even go further

Re: [gmx-users] POSRES for umbrella sampling

On 3/15/17 6:19 AM, stellatof wrote: Dear all, I have a question regarding the use of "POSRES" in . In the umbrella sampling tutorial it says that POSRES is used to keep one chain as an immobile reference in the pulling procedure. What is the effect of POSRES? Does it keep the molecule center

[gmx-users] Gromacs installation on GPU

Dear Gromacs users, I had installed gromacs using following commands: tar xvf cmake-3.6.1.tar.gz tar xvzf gromacs-5.1.3.tar.gz cd ../cmake-3.6.1. ./configure make make install cd ../gromacs-5.1.3 mkdir build cd build cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON

[gmx-users] Distance restraints on two TYR OH groups so that they are together

Hello, I try to add distance restraints on two TYR OH groups so that they are together in the end like this: [ distance_restraints ]  195 281 1 1 1 0.2 0.22 0.24 1000 But it does not work at least over time frame I tested, they even go further away from each other. Here I share my all

[gmx-users] POSRES for umbrella sampling

Dear all, I have a question regarding the use of "POSRES" in . In the umbrella sampling tutorial it says that POSRES is used to keep one chain as an immobile reference in the pulling procedure. What is the effect of POSRES? Does it keep the molecule center of mass fix or does it restrain the