Re: [gmx-users] Excessive and gradually increasing memory usage with OpenCL

Hi, Our own installation guide does advise against OpenCL on NVIDIA hardware, and also hints that compiler compatibility is dependent on the CUDA version, but we could improve the latter I think. Last time we considered performance of OpenCL on NVIDIA, the GPU kernels seemed to always run

Re: [gmx-users] Excessive and gradually increasing memory usage with OpenCL

Thank you for this workaround! Just setting the GMX_DISABLE_GPU_TIMING environment variable has allowed mdrun to progress for several million steps. The memory usage is still high at about 1 GB memory and 26 GB swap, but it does not appear to increase as the simulation progresses. I tried 6

[gmx-users] RDF brads

Dear all, To obtain the coarse-graine (CG) parameters of a molecule using votca, below are the considered beads: (the bead are weighted by atomic weights ) Bead A contains atoms of " a1, ..., a11" Bead B contains atoms of " b1, ..., b9" Bead C contains atoms of " c1,..., c13" Now, to calculate

Re: [gmx-users] Performance

Does it work? https://drive.google.com/open?id=1n5m1tNGbnV7oZnuAEgZ7gSP6qA6HluNl How about this? Myunggi Yi On Wed, Mar 28, 2018 at 12:20 PM, Mark Abraham wrote: > Hi, > > Attachments can't be accepted on the list - please upload to a file sharing > service and

[gmx-users] Problems in putting restraints during free energy perturbation calculations (cont)

Hi, I would like to follow-up on this: https://www.mail-archive.com/gromacs.org_gmx-users@maillist.sys.kth.se/msg31701.html. I already fixed the problem with the coulombic and vdW interactions with the help of Mark (thank you!). However, my problem now is on turning off the restraints from

Re: [gmx-users] Performance

I see. I am trying again. ​ ves ​ Myunggi Yi (이명기, Ph. D.), Professor Department of Biomedical Engineering (의공학과 bme.pknu.ac.kr), College of Engineering Interdisciplinary Program of Biomedical Mechanical & Electrical

Re: [gmx-users] Performance

Hi, Attachments can't be accepted on the list - please upload to a file sharing service and share links to those. Mark On Wed, Mar 28, 2018 at 6:16 PM Myunggi Yi wrote: > I am attaching the file. > > Thank you. > > Myunggi Yi > > On Wed, Mar 28, 2018 at 11:40 AM,

Re: [gmx-users] Performance

I am attaching the file. Thank you. Myunggi Yi On Wed, Mar 28, 2018 at 11:40 AM, Szilárd Páll wrote: > Again, please share the exact log files / description of inputs. What > does "bad performance" mean? > -- > Szilárd > > > On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi

Re: [gmx-users] Performance

Again, please share the exact log files / description of inputs. What does "bad performance" mean? -- Szilárd On Wed, Mar 28, 2018 at 5:31 PM, Myunggi Yi wrote: > Dear users, > > I have two questions. > > > 1. I used to run typical simulations with the following command.

Re: [gmx-users] mdrun on single node with GPU

Hi, I can't reproduce your issue, can you please share a full log file, please? Cheers, -- Szilárd On Wed, Mar 28, 2018 at 5:26 AM, Myunggi Yi wrote: > Dear users, > > I am running simulation with gromacs 2018.1 version > on a computer with quad core and 1 gpu. > > I

[gmx-users] Performance

Dear users, I have two questions. 1. I used to run typical simulations with the following command. gmx mdrun -deffnm md I had no problem. Now I am running a simulation with "Dry_Martini" FF with the following input. integrator = sd tinit= 0.0 dt

[gmx-users] ss.xpm file: first residue showing first, or last residue showing first?

Dear Gromacs, In the ss.xpm file for secondary structures, can I ask if the first residue shows first, or last residue shows first? Is this already written in the file? I also have a chain separator. Can I ask does it show in the beginning or between the two chains? (Sorry, I asked this

Re: [gmx-users] Umbrella sampling: window distance - harmonic force constant

Okay. Thanks Justin! On 27.03.2018 21:12, Justin Lemkul wrote: On 3/27/18 4:44 AM, Hermann, Johannes wrote: Dear All, dear Justin, I am playing around with my umbrella sampling setup and I was looking at your paper which you linked in your umbrella sampling tutorial ("Assessing the

Re: [gmx-users] RMSD values consideration

Try using trjconv to remove pbc before analysis Regards,Ahmed On Wed, 28 Mar, 2018 at 8:43 am, SHYANTANI MAITI wrote: Dear all, After using this command for computation of rmsd of backbone of protein protein complex consisting of three proteins :

[gmx-users] RMSD values consideration

Dear all, After using this command for computation of rmsd of backbone of protein protein complex consisting of three proteins : /home/locuz/apps/gromacs/5.1/bin/gmx_mpi rms -f md_0_1.trr -s md_0_1.tpr The rmsd is drastically increasing from 1 to 6 nm and after that it again decreases to 1nm. can