Re: [gmx-users] domain decomposition Error

Hi, There's good advice for this problem at think link that was suggested in the error message: http://www.gromacs.org/Documentation/Errors. Probably your box volume or NpT protocol need some attention. Mark On Tue, 7 Mar 2017 06:23 shweta singh wrote: > Thank you ! >

[gmx-users] NPT equillabration Error bilayer

I am trying to run a lipid bilayer simulation but during the npt equillibration step I am getting the following error "1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y" I have successfully run the

Re: [gmx-users] domain decomposition Error

Thank you ! On Tue, Mar 7, 2017 at 9:47 AM, MRINAL ARANDHARA < arandharamri...@iitkgp.ac.in> wrote: > I am trying to run a lipid bilayer simulation but during the npt > equillibration step I am getting the following error > "1 particles communicated to PME rank 6 are more than 2/3 times the >

[gmx-users] unusual GridMAT-MD tool result using gnuplot

Dear gmx users, I used the GridMAM-MD tool (v2) for the membrane thickness. After the gridmat-md, I used gnuplot for visualization. But there is no surface figure, there are bar code like lines. How can I fix these error? ​ thickness.bmp

[gmx-users] Domain Decomposition Error

I am trying to run a lipid bilayer simulation but during the npt equillibration step I am getting the following error "1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y" I have successfully run the

[gmx-users] domain decomposition Error

I am trying to run a lipid bilayer simulation but during the npt equillibration step I am getting the following error "1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y" I have successfully run the

Re: [gmx-users] Your confirmation is required to join the gromacs.org_gmx-users mailing list

I am trying to run a lipid bilayer simulation but during the npt equillibration step I am getting the following error "1 particles communicated to PME rank 6 are more than 2/3 times the cut-off out of the domain decomposition cell of their charge group in dimension y" I have successfully run the

Re: [gmx-users] running MD on gpu (Fatal error)

Hi, Somehow your execution environment has eg OMP_NUM_THREADS set to 192. That would be most likely through misuse of your MPI run command, or job scheduler. But we can't see enough of the GROMACS log output to know any more. Mark On Mon, 6 Mar 2017 19:57 Andrew Bostick

[gmx-users] running MD on gpu (Fatal error)

Dear Gromacs users, I am running MD on gpu using following command line: gmx_mpi mdrun -nb gpu -v -deffnm gpu_md But, I encountered with: GROMACS version:VERSION 5.1.3 Precision: single Memory model: 64 bit MPI library:MPI OpenMP support: enabled

Re: [gmx-users] Analyzing Desmond trajectories using GROMACS tools

On 06/03/17 17:53, zeineb SI CHAIB wrote: Dear Justin, Again, thank you very much for your fast reply, which is very clear. However, I'm having difficulties to understand how the tools that I'll use will not depend on the force field parameters. For example, I'll use gmx_order to compute

Re: [gmx-users] Analyzing Desmond trajectories using GROMACS tools

Dear Justin, Again, thank you very much for your fast reply, which is very clear. However, I'm having difficulties to understand how the tools that I'll use will not depend on the force field parameters. For example, I'll use gmx_order to compute the order parameter per atom for carbon

Re: [gmx-users] fatal error

Hi, pdb2gmx isn't magic. You have to to choose a force field that has an .rtp file that has residue definitions that match what's in your coordinate file. We currently can't know at which stage of this process the problem is. :-) Mark On Mon, Mar 6, 2017 at 4:23 PM Urszula Uciechowska <

Re: [gmx-users] fatal error

On 3/6/17 10:23 AM, Urszula Uciechowska wrote: Hi, I do not know. After running pdb2gmx I am not getting the .itp file for the DC5... I am using gromacs 5.0.4. What can be wrong here? Did you check the .rtp for DC5, as Mark suggested? Based on your knowledge of DNA structure, why might

Re: [gmx-users] Analyzing Desmond trajectories using GROMACS tools

On 3/6/17 10:16 AM, zeineb SI CHAIB wrote: Dear Justin, Thank you very much for your help and clarifications. I have a question please: I used OPLS-3 force field when running my simulations with Desmond, which is absent in GROMACS 5.1.3 In order to generate the topology (protein and POPC),

Re: [gmx-users] fatal error

Hi, I do not know. After running pdb2gmx I am not getting the .itp file for the DC5... I am using gromacs 5.0.4. What can be wrong here? Urszula > Hi, > > What name does the .rtp entry for DC5 use for its phosphorus atom? > > Mark > > On Mon, Mar 6, 2017 at 1:39 PM Urszula Uciechowska < >

Re: [gmx-users] Analyzing Desmond trajectories using GROMACS tools

Dear Justin, Thank you very much for your help and clarifications. I have a question please: I used OPLS-3 force field when running my simulations with Desmond, which is absent in GROMACS 5.1.3 In order to generate the topology (protein and POPC), I guess I have to work with the same force

Re: [gmx-users] Meaning of columns in .xvg output file

On 3/6/17 5:36 AM, Kamps, M. wrote: Dear gmx-users, I've got a small question of which I can't find the answer. I have a simulation where I want to calculate the average velocity of certain particles. I've created an output .xvg file via the command: gmx traj -f input.trr -s input.tpr -n

Re: [gmx-users] fatal error

Hi, What name does the .rtp entry for DC5 use for its phosphorus atom? Mark On Mon, Mar 6, 2017 at 1:39 PM Urszula Uciechowska < urszula.uciechow...@biotech.ug.edu.pl> wrote: > Dear gmx users, > > After running a pdb2gmx script of the pdb file I am getting an error > message: > > > Fatal

[gmx-users] fatal error

Dear gmx users, After running a pdb2gmx script of the pdb file I am getting an error message: Fatal error: Atom P in residue DC 2 was not found in rtp entry DC5 with 28 atoms while sorting atoms. The DC 2 in pdb file: TER 11412 LEU B 366 ATOM 11413 P DC C 2 0.997 17.702

[gmx-users] Meaning of columns in .xvg output file

Dear gmx-users, I've got a small question of which I can't find the answer. I have a simulation where I want to calculate the average velocity of certain particles. I've created an output .xvg file via the command: gmx traj -f input.trr -s input.tpr -n input.ndx -av output.xvg My output, is as

Re: [gmx-users] NPT equilibration without pbc

Hi, People might find the approach at https://doi.org/10.1017/jfm.2015.517 more rigorous! Mark On Mon, Mar 6, 2017 at 1:58 AM Rajorshi Paul wrote: > Thanks Alex for the suggestion!! > > On 5 March 2017 at 01:49, Alex wrote: > > > I looked

Re: [gmx-users] To invoke GPU in gromacs version 4.6.4

Hi, Yes, you need to install GROMACS with GPU support, and you should do so with a more recent version that is still supported, has fewer bugs, and runs faster, eg http://manual.gromacs.org/documentation/ Mark On Mon, Mar 6, 2017 at 9:03 AM Alex wrote: > Well, the info

Re: [gmx-users] To invoke GPU in gromacs version 4.6.4

Well, the info you received is sufficient to figure out what happened. Install latest CUDA driver, install the latest version of Gromacs with GPU support. http://www.gromacs.org/Documentation/Installation_Instructions_5.0#typical-gromacs-installation Files do not get attached here and your