[gmx-users] g_mindist for hydrophobic interactions

Dear All, I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a cross talk for receptor's transactivation. Is g_mindist a good tool for this purpose? Do you have more suggestions? Moreover, should I use trjconv for pbc treatment before

[gmx-users] (no subject)

Dear gmx users I am performing a simulation by gromacs. for building the ligand itp file by Prodrg, I get an error thet boron atom is not supported by this program. Do you have any propose for solute this problem? regards -- Somayeh Alimohammadi Ph.D Student of Medical Nanotechnology Shahid

Re: [gmx-users] g_mindist for hydrophobic interactions

Another option is g_hbond -contact. On 8 Sep 2014, at 09:25, Ca C. devi...@hotmail.com wrote: Dear All, I have to verify if some hydrophobic residues, during the simulation, conserve their interactions and make a cross talk for receptor's transactivation. Is g_mindist a good tool for this

[gmx-users] GPU job failed

Hello: I am trying to use the following command in Gromacs-5.0.1: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host cudaB: #0: NVIDIA GeForce GTX 780 Ti, compute cap.: 3.5, ECC: no,

[gmx-users] g-select failed

Hello: I am trying to make two groups for my lipids sytem by g_select with command line: g_select_mpi -sf select.dat -f em.gro here is the content of select.dat: up=z80; down=z80; but it failed with messages: Program: gmx select, VERSION 5.0.1 Source file:

[gmx-users] Status of MD simulation

hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how to check the status of simulation in between the run whether it is going in right direction or not? thanks regards ankit -- Gromacs Users mailing list * Please search the

Re: [gmx-users] g-select failed

Hi, On Mon, Sep 8, 2014 at 4:47 PM, Albert mailmd2...@gmail.com wrote: I am trying to make two groups for my lipids sytem by g_select with command line: g_select_mpi -sf select.dat -f em.gro here is the content of select.dat: up=z80; down=z80; but it failed with messages: ... Your

[gmx-users] Integrator problem

Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got error of more force on one atomI not clear why this is happeingcan any body guide me please.. Regards

Re: [gmx-users] Status of MD simulation

Make a temporary copy of the files (generally not necessary, but might help) and observe whatever suits you. Mark On Sep 8, 2014 3:50 PM, ankit agrawal aka...@gmail.com wrote: hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how

Re: [gmx-users] Status of MD simulation

Hi...I think the best way is to check log file If I m wrong please do correct me!! Regards Lovika On 8 Sep 2014 19:21, ankit agrawal aka...@gmail.com wrote: hi I am running a 5ns simulation using mdrun command. So this will take a day to complete. So I want to know that how to check the

Re: [gmx-users] Integrator problem

The md integrator does MD, not EM... Mark On Sep 8, 2014 4:11 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyoneI want to ask one question...In my .mdp file if I use md intergrator for energy minimisation .then system is fine...but if I use steep integrator...my system got

Re: [gmx-users] g-select failed

Hello Teemu: thanks a lot for such helpful advices. It works now. If I would like to select protein and z80, I use following select.dat file: up protein and z80; down protein and z80; but it failed with messages: In command-line option -sf Error in parsing selections from file

Re: [gmx-users] GPU and MPI

I have found my mistake and hopefully this information is useful. This is caused by pinning of OPENMP threads by MPI. By default, all OPENMP threads belongs to each MPI rank will run on one core only in our cluster. I didn't realize this partially because Gromacs's thread MPI (this is employed

Re: [gmx-users] Integrator problem

Oo.thanks for guiding Mark !!! Regards Lovika On 8 Sep 2014 19:45, Mark Abraham mark.j.abra...@gmail.com wrote: The md integrator does MD, not EM... Mark On Sep 8, 2014 4:11 PM, Lovika Moudgil lovikamoud...@gmail.com wrote: Hi everyoneI want to ask one question...In my .mdp file

Re: [gmx-users] GPU and MPI

Now the question is how can we solve the problem in GPU workstaton and make two GPU work together for one task? thx Albert On 09/08/2014 04:18 PM, Da-Wei Li wrote: I have found my mistake and hopefully this information is useful. This is caused by pinning of OPENMP threads by MPI. By

[gmx-users] Performing MD simulations in presence of trivalent cations.

Hello gmx users, I am currently working on the ion dependent persistence length calculations of RNA strands.I want to calculate it in presence of multivalent cations like Al3+ and Co3+. I guess in order to do that we have to include the specifications of these ions

[gmx-users] protein-ligand complex by gromacs

hi GMX users i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. I've checked all of the input files and the steps , but I did

Re: [gmx-users] Performing MD simulations in presence of trivalent cations.

On 2014-09-08 18:28, soumadwip ghosh wrote: Hello gmx users, I am currently working on the ion dependent persistence length calculations of RNA strands.I want to calculate it in presence of multivalent cations like Al3+ and Co3+. I guess in order to do that we have to

Re: [gmx-users] no data read from file pdo.gz

On 9/8/14 12:36 AM, Lyna Luo wrote: Hi Justin, The blank between lines are just from email format. I used only one window to see if g_wham can readin my data, but I actually have 64 window. Please see the error message below. Thanks again! -Lyna GROMACS: gmx wham, VERSION 5.0

Re: [gmx-users] protein-ligand complex by gromacs

On 9/8/14 12:30 PM, Mahboobeh Eslami wrote: hi GMX users i have simulated the protein-ligand complex by gromacs. I've repeated the simulation twice but i have get very different results. in one of the simulations ligand separated from protein and stayed in the center of box. I've checked

[gmx-users] Limitation on the maximum number of OpenMPI threads

Hello, I was trying to run a simulation on Gromacs-4.6.3 which has been compiled without thread MPI on a BlueGene/Q system. The configurations per node are as follows: PowerPC A2, 64-bit, 1.6 GHz, 16 cores SMP, 4 threads per core For running on 8 nodes I tried: srun mdrun_mpi -ntomp 64 But,

Re: [gmx-users] GPU and MPI

Helo Yunlong: thx a lot for the reply. It works in Gromacs-4.6.5, but it does NOT in Gromacs-5.0.1. I used the following command: mpirun -np 2 mdrun_mpi -v -s npt2.tpr -c npt2.gro -x npt2.xtc -g npt2.log -gpu_id 01 -ntomp 10 but it always failed with messages: 2 GPUs detected on host

[gmx-users] electric filed

Hello: I am simulating a protein in lipids bilyaer and I am going to apply 50mV voltage across the bilayer. I noticed this paper: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056342 The author did in Gromacs. I noticed that there is a Electric fieldselectric field

Re: [gmx-users] GPU and MPI

Hi, Albert I think the error message is very clear. You have one MPI rank per node, but provide 2 GPUs per node. The gpuid argument is applied on each of the node. dawei On Mon, Sep 8, 2014 at 2:38 PM, Albert mailmd2...@gmail.com wrote: Helo Yunlong: thx a lot for the reply. It works in

Re: [gmx-users] GPU and MPI

HI Dawei: Yes, it is. I am running it in a workstation which have 1 CPU (20 cores) plus 2 GPU. It is not a server. That's why I use additional option: -ntomp 10 So that each MPI rank can use 10 core CPU. This works fine in Gromacs-4.6.5, but it doesn't work in 5.0.1 thx Albertt On

Re: [gmx-users] GPU and MPI

Hi, Albertt It is quite strange. Your log file should provide how many MPI ranks and how many OPENMP threads per rank. Can you check that part to find how many MPI ranks are there? best, dawei On Mon, Sep 8, 2014 at 3:18 PM, Albert mailmd2...@gmail.com wrote: HI Dawei: Yes, it is. I am

[gmx-users] PME

Dear GMX Users I have a question about PME loading When executing mdrun. All my MD simulations (DNA-ligand interaction in triclinic box) are computed on in-house Linux 64-bit Intel Core-i7. According to gromacs tutorial in Justin web site

[gmx-users] [ANN] MDTraj 1.0: Trajectory Analysis in Python

Hello, We are happy to announce the 1.0 release of MDTraj. MDTraj is a modern, lightweight and efficient software package for analyzing molecular dynamics trajectories. It reads and writes trajectory data from a wide variety of formats, including those used by AMBER, GROMACS, CHARMM, NAMD and

Re: [gmx-users] GPU job failed

Hi, It looks like you're starting two ranks and passing two GPU IDs so it should work. The only think I can think of is that you are either getting the two MPI ranks placed on different nodes or that for some reason mpirun -np 2 is only starting one rank (MPI installation broken?). Does the same

Re: [gmx-users] PME

Hi, By default, there will be no separate PME ranks used with less than AFAIR 12 ranks (i.e. the default with small number of ranks is -npme 0). Without separate PME ranks (and without GPUs) there is no PP-PME load balance to tweak, so the PME load is not very relevant from performance

Re: [gmx-users] GPU job failed

Same idea with Szilard. How many nodes are you using? On one nodes, how many MPI ranks do you have? The error is complaining about you assigned two GPUs to only one MPI process on one node. If you spread your two MPI ranks on two nodes, that means you only have one at each. Then you can't

[gmx-users] [CfP] 5th International Workshop on Model-driven Approaches for Simulation Engineering (Mod4Sim)

# 5th International Workshop on Model-driven Approaches for Simulation Engineering part of the Symposium on Theory of Modeling and Simulation (SCS SpringSim 2015) CALL

Re: [gmx-users] Limitation on the maximum number of OpenMPI threads

Hi, Generally speaking, in the absence of accelerators, OpenMP as used in GROMACS 4.6/5.0 is only useful as you get down to around a few hundred atoms per core (details vary, but since you often can't get fewer than 512 cores of BG/Q the point is often moot there), and only at fairly low OpenMP

Re: [gmx-users] GPU job failed

thanks a lot for reply both Yunlong and Szilard. I don't set up PBS system and nodes in the workstation. In the GPU workstation, it contains 1 CPU with 20 cores, and two GPUs. So it is similar to 1 nodes with 2 GPUs. But I don't know why 4.6.5 works, but 5.0.1 doesn't ... Thx again

Re: [gmx-users] Query regarding the addition of solvent molecule

Hi, I have included the link to my dropbox where I have attached my gromacs topology files. Though I have included the cyclohexane itp file in the .top file still I am the same error NO SUCH MOLECULETYPE CHX. SO, Kindly need help in this regard. Thank you in advance.