[gmx-users] Water naming

Dear users, I was analysing the hydrogen bonding interaction of proteins and water in a simulation and was trying to extract specific water that forms hbond using matrix and index files generated by g_hbond. But I found that the index file created using g_hbond has continuous water labels byt the

[gmx-users] .gro File manipulation

Dear Gromacs Users, I hava a membrane channel in a .gro file, but the -n and -c terminal are bigger, i mean the channel box is bigger( in x and y) than the membrane (512 POPC) , my 512 POPC is created using genconf with a 128POPC so i create a 1152 POPC with genconf nbox 3 3 1 , but there are to

Re: [gmx-users] multiple GPU on multiple nodes

Hi guys Thanks for your help. It is finally working !!! The performance is increased more than 2.5X that just using CPUs. I was able to test up to 64 nodes (64 gpu, 256 cpus). The idea of the aprun -cc none was the one that give me this great performance. I still do not understand the rank id

[gmx-users] counter ion and charged polymer in gas-phase

Hi,   I am doing simulation of charged polymer . When I do the simulation in water or solvent, I put counter ion in the solvent to neutralize the charge in the system. But, if I want to do the simulation in gas-phase ( i.e no solvent), does adding counter-ion make any sense or is it realistic? I

[gmx-users] Opinions on Copernicus to streamline Gromacs workflows?

Hello, In my group people are thinking about using Copernicus ( http://copernicus-computing.org/about/ ) to streamline Gromacs workflows, especially with the perspective of doing ensemble MD simulations. I remember having heard the author in a seminar presenting it, and it looked extremly int

Re: [gmx-users] Number of coordinate in pr.top and solv.gro not matching

On 2/12/14, 12:33 PM, mabbasi wrote: dear all I am doing MD simulation of ligand-protein by GROMACS Tutorial for Drug – Enzyme Complex. I have done below steps: From the steps listed below, you are probably following some very old version of the tutorial by John Kerrigan. He has updated t

[gmx-users] Number of coordinate in pr.top and solv.gro not matching

dear all I am doing MD simulation of ligand-protein by GROMACS Tutorial for Drug – Enzyme Complex. I have done below steps: Use the Dundee PRODRG server to build a Gromacs89 topology for ligand. Rename the DRGGMX.ITP file to drg.itp (No errors in atom typing were found). Process the pr.pdb fi

Re: [gmx-users] GPU job often tailed

Do you have a factory-overclocked model? Even if you don't if you happen to run Windows or if you are experienced with custom BIOS-es, you could try lowering the GPU clock frequency a bit and see if the error still occurs. You may also want to increase the GPU fan speed, the default fan profile on

Re: [gmx-users] Exclude Coulomb interactions among certain atoms in SWM4 water molecule

On 2/12/14, 12:52 AM, Sandipan Dutta wrote: Dear GMX users: I am fairly new to gromacs. I am trying to simulate SWM4 water model. In the model the electrostatic interactions between the Drude particle (DOH2) and oxygen atom (OP) are excluded. I have created an index file index.ndx that contain

Re: [gmx-users] question

On 2/12/14, 6:40 AM, nafas wrote: Thank you very much. Do you recommend that I do inflate and shrink step for my project?? I know nothing about the project. As I said before, build the system however you like based on (1) what makes sense to you, (2) what you can defend to reviewers, and

Re: [gmx-users] GPU job often tailed

I am using GTX690. OK, I will do some test. thank you for helpful advices. Albert On 02/12/2014 01:54 PM, Szilárd Páll wrote: Your mail reads like an FYI, what is the question? In case if you were wondering what causes this, it could be simply a soft error, but it's hard to tell. What GPU a

Re: [gmx-users] GPU job often tailed

Your mail reads like an FYI, what is the question? In case if you were wondering what causes this, it could be simply a soft error, but it's hard to tell. What GPU are you running on? If it's in your own workstation, you could consider running a longer stress-test on it using e.g. CUDA memtest. -

Re: [gmx-users] question

On 2/12/14, 3:08 AM, nafas wrote: Hi Justin. I hope you have a nice day I would like to simulate a peptide on the membrane .In tutorial gromacs that simulate peptide KALP_15 in membrane DPPC ,you use inflate and shrink step.Do I need to do this step for my system? Build the system however

Re: [gmx-users] Protein - Ligand simulation

On 2/12/14, 3:35 AM, lucaam86 wrote: Thank you for your reply. Yes, I'm not specialist and I'm introducing now in Molecular Simulation. I don't know Steered Molecular Dynamic, do you have tutorials or guide documentations for it? Could you explain why the tutorial suggested by Aldo is not indic

Re: [gmx-users] "Justifying" 4fs production runs after 1fs equilibrations?

Hi, Highly unlikely. The point of equilibration is to move from some point near > the ensemble, to some point in the ensemble, perhaps without perturbing the > starting structure significantly. The last phase of equilibration should > match the production ensemble (or simply be subtracted from the

[gmx-users] GPU job often tailed

Hello: I noticed that my GPU job often failed from time to time, here is the informations: --- Program mdrun_mpi, VERSION 4.6.5 Source code file: /home/albert/install/source_code/gromacs-4.6.5/src/mdlib/nbnxn_cuda/nbnxn_cuda.cu, line: 591

Re: [gmx-users] Protein - Ligand simulation

Thank you for your reply. Yes, I'm not specialist and I'm introducing now in Molecular Simulation. I don't know Steered Molecular Dynamic, do you have tutorials or guide documentations for it? Could you explain why the tutorial suggested by Aldo is not indicated for me? Sorry for my lack of prepara

[gmx-users] question

Hi Justin. I hope you have a nice day I would like to simulate a peptide on the membrane  .In tutorial gromacs that simulate peptide KALP_15 in membrane DPPC ,you use inflate and shrink step.Do I need to do this step for my system? May you can help me؟ Thanks -- Gromacs Users mailing list * P

Re: [gmx-users] (no subject)

Hi Justin. I hope you have a nice day I would like to simulate a peptide on the membrane  .In tutorial gromacs that simulate peptide KALP_15 in membrane DPPC ,you use inflate and shrink step.Do I need to do this step for my system? May you can help me؟ Thanks On Wednesday, February 12, 2014