Re: [gmx-users] regarding MSD

Hello I have posted the query earlier but havent got any reply and so reposting it again. I have read few papers that determine transition temperature from the plot of average MSD of hydrogen atoms of protein versus temperature. My question is: At a particular temperature, we get a linear curve

[gmx-users] Why we are not using GPU to solve FFT?

Hi, I wonder why we are using cpu instead of gpu to solve FFT? Is it possible to use gpu fft library, say cuFFT to make the FFT used in PME faster? BR, Theo -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before

[gmx-users] regarding g_hydorder

Hello all I would like to calculate both distance and angle water orientational order. I have made an index file containing all oxygen atoms of water and used trjorder as: g_hydorder -f *.xtc -s *.tpr -n *.ndx -o file1_1 file2_1 -or file1_2 file2_2 How to interpret the results of the output

Re: [gmx-users] Why we are not using GPU to solve FFT?

On Fri, Aug 22, 2014 at 9:10 AM, Theodore Si sjyz...@gmail.com wrote: Hi, I wonder why we are using cpu instead of gpu to solve FFT? While people continue to attach GPUs to nodes with tasty x86 cores, we'd like to use them. Adding more work to the GPU while leaving the CPU idle does not

Re: [gmx-users] Can we set the number of pure PME nodes when using GPUCPU?

Hi Mark, Could you tell me why that when we are GPU-CPU nodes as PME-dedicated nodes, the GPU on such nodes will be idle? Theo On 8/11/2014 9:36 PM, Mark Abraham wrote: Hi, What Carsten said, if running on nodes that have GPUs. If running on a mixed setup (some nodes with GPU, some not),

[gmx-users] (no subject)

Dear Users, generally for running a 10 ns simulation is there any online server facility available. This will be helpful for people who do not have a continuous access to the server. regards Suriyanarayanan -- Gromacs Users mailing list * Please search the archive at

[gmx-users] ligand is out side the box

hello gromacs users i am working on protein ligand complex with POPC membrane according to justin (from previous mail) i built the system without ligand and after minimization and shrink paste the ligand and edit the box size but after solvation and water addition ligand is out side the box

[gmx-users] pme ranks

Does anyone know that what the pme ranks mean? xiexiao...@sjtu.edu.cn -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe

Re: [gmx-users] pme ranks

On 22 Aug 2014, at 12:48, xiexiao...@sjtu.edu.cn wrote: Does anyone know that what the pme ranks mean? See for example [1] in the section Multiple-Program, Multiple-Data PME Parallelization. Best, Carsten 1. Hess, B., Kutzner, C., van der Spoel, D. Lindahl, E. GROMACS 4: Algorithms

Re: [gmx-users] Can we set the number of pure PME nodes when using GPUCPU?

Hi, Because no work will be sent to them. The GPU implementation can accelerate domains from PP ranks on their node, but with an MPMD setup that uses dedicated PME nodes, there will be no PP ranks on nodes that have been set up with only PME ranks. The two offload models (PP work - GPU; PME work

Re: [gmx-users] Extending simulation problem.

2014-08-21 17:45 GMT+01:00 Mark Abraham mark.j.abra...@gmail.com: Well in my *log file nothing about state or *cpi files is mentioned. Sounds like perhaps your combination of circumstances (-append, no old output files provided for appending, maybe not even a checkpoint file provided) is

Re: [gmx-users] Extending simulation problem.

Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing statusfile with starting step 0 and length

Re: [gmx-users] Extending simulation problem.

On 8/22/14, 8:49 AM, Dawid das wrote: Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending remaining runtime of by 95000 ps (now 5000 steps) Writing

[gmx-users] QM/MM simulation: point-charge, pbc and bOPT=yes problems

Dear Gromacs users! I'm trying to interface gromacs (5.0) with orca (2.9.1), although i encountered some problems. I'm testing a tripeptide system which i found here: http://www.picb.ac.cn/~liwenjin/QMMM_simulations/index.html , but i'm using a different .mdp file, with these parameters (i copied

Re: [gmx-users] Interpreting flooding results

Hello Carsten, thanks for replying. Yes, I'm using GMX 4.6.5, so I'm able to see the info in the .xvg file. Best, --- Biological Chemistry and Physics Faculty of Pharmaceutical Sciences at Ribeirão Preto University of São Paulo - Brazil - Mensagem original - De: Carsten Kutzner

Re: [gmx-users] Extending simulation problem.

On Aug 22, 2014 2:51 PM, Justin Lemkul jalem...@vt.edu wrote: On 8/22/14, 8:49 AM, Dawid das wrote: Can you just have a quick look at this? When I run: tpbconv -s npt-md.tpr -extend 95000 -o npt-md.tpr to extend simulation by 95 ns this time I got this message at the end: Extending

Re: [gmx-users] QM/MM simulation: point-charge, pbc and bOPT=yes problems

Hi, Unfortunately the QM/MM interface is completely unmaintained, so the fact that it doesn't set fire to your chair is something of a bonus! If you can get the group scheme to do something useful, that's great, but I would suggest you build an older version of GROMACS. In practice, with the

Re: [gmx-users] Numerical Stability of Gromacs Implementation

On Aug 22, 2014 4:49 PM, Johnny Lu johnny.lu...@gmail.com wrote: it has many (relatively) power7 cores and aix 6.1.0.0 with no gpu, and I compiled single precision gromacs 4.6.6 with open mp on it. I tried xlc or mpcc for 30+ times. 6.1 was released 7 years ago, but if you have a functional

Re: [gmx-users] Job Submission script for Multiple nodes GPUs

There will be an error if I did mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 01 -nb gpu -ntomp 6 Incorrect launch configuration: mismatching number of PP MPI processes and GPUs per node. mdrun_mpi was started with 4 PP MPI processes per node, but you

Re: [gmx-users] Job Submission script for Multiple nodes GPUs

On 22 Aug 2014, at 18:09, Xingcheng Lin linxingcheng50...@gmail.com wrote: There will be an error if I did mpiexec -np 4 mdrun_mpi -s run.tpr -cpi state.cpt -cpo state.cpt -noappend -gpu_id 01 -nb gpu -ntomp 6 Incorrect launch configuration: mismatching number of PP MPI processes and

[gmx-users] Elastic Network Model

Hello All, I have a quick question regarding Elastic Network model. If the define RUBBER BANDS option is not stated in the .top file, the .itp file (with conditions for if elastic network is on) is same as if it was made with without any elastic network? Please guide. Thanks, sxn -- Gromacs

Re: [gmx-users] Elastic Network Model

Hi sxn, Rubber bands... :) So you're talking about a CG topology. If RUBBER_BANDS is not defined, the network is not active. However, they can also be defined in the .mdp file. Furthermore, if you're talking about ElneDyn, then the model is not like regular Martini if you disable the elastic

Re: [gmx-users] (no subject)

Hi Suriyanarayanan, You can check out the WeNMR Gromacs portal. Hope it helps, Tsjerk On Aug 22, 2014 10:29 AM, Balasubramanian Suriyanarayanan bsns...@gmail.com wrote: Dear Users, generally for running a 10 ns simulation is there any online server facility available. This will be

[gmx-users] build membrane system from Charmm-Gui

Hi All,  I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with pdb2gmx to get top file (I used charmm36), then I would like to know, how to add water and ions back to the system? I read the

Re: [gmx-users] build membrane system from Charmm-Gui

On 8/22/14, 4:36 PM, Xiang Ning wrote: Hi All, I am using POPC/POPG mixed membrane built by Charmm-gui. After remove ions and water from CHARMMGUI pdb and save just the membrane pdb, and use this pdb with pdb2gmx to get top file (I used charmm36), then I would like to know, how to add