[gmx-users] Different fudge scaling against the default ones

Dear gmx users, I see the following lines in the forcefield.itp file of amberGS.ff (gmx 466) (share/gromacs/top/amberGS.ff/) : ;-- #define _FF_AMBER #define _FF_AMBER94 [ d

[gmx-users] Can I calculate free energy of Tutorial 1 of Justin's tutorials?

Dear gmx users, Can I calculate free energy of Tutorial 1 of Justin's tutorials? Batsaikhan -- 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

[gmx-users] Using a 4.6.5 cpt file in 5.0 to extend a run?

Hi all, I am trying to extend some simulations done on the XSEDE Trestles system over the summer, and they have upgraded to 5.0 since then from 4.6.5. Can anyone give any tips for navigating around the below error? Program mdrun_mpi, VERSION 5.0 Source code file: /state/partition1/git/chemistry-

Re: [gmx-users] Different cutoffs for different interactions?

On 9/24/14 3:54 PM, Aranha, Michelle wrote: Hi all, Is it possible to use different cut-off radius values for different pair (atom-atom) interactions in GROMACS. I understand that this is not recommended but I need to try this for my system. You could probably achieve this with tabulated

[gmx-users] Different cutoffs for different interactions?

Hi all, Is it possible to use different cut-off radius values for different pair (atom-atom) interactions in GROMACS. I understand that this is not recommended but I need to try this for my system. Best regards, Michelle -- Gromacs Users mailing list * Please search the archive at http://

Re: [gmx-users] apoenzyme wanted

On 9/24/14 1:36 PM, N. S. wrote: Dear Gromacs users, I study an enzyme (hydrolase), which is known to undergo some conformational changes upon substrate or inhibitor binding. Protein Data Bank at rcsb.org has only suitable entries with complex enzyme-inhibitor structures. I had got might be a

Re: [gmx-users] How can I select a group number automatically

And there are even more options at http://www.gromacs.org/Documentation/How-tos/Using_Commands_in_Scripts Mark On Wed, Sep 24, 2014 at 3:58 PM, Xiaobin Cao wrote: > Thank you, Erik and Chandan. They all work well. They will save me a lot > of time. > > __

[gmx-users] apoenzyme wanted

Dear Gromacs users, I study an enzyme (hydrolase), which is known to undergo some conformational changes upon substrate or inhibitor binding. Protein Data Bank at rcsb.org has only suitable entries with complex enzyme-inhibitor structures. I had got might be a stupid idea to make minimisation and

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

what happened when you ran without gpu? I installed 5.0.1 on a single machine without gpu. It used threaded mpi and no real mpi and ran fine. On Wed, Sep 24, 2014 at 12:21 PM, Johnny Lu wrote: > well... I think i read it somewhere that threaded MPI is a dropped in > replacement for real MPI. Ope

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

well... I think i read it somewhere that threaded MPI is a dropped in replacement for real MPI. OpenMPI is a real MPI. So those two shouldn't be compatible. I think we chose that when we compiled gromacs (whether we use real MPI or not). Threaded MPI is enabled by default if we didn't compile for g

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

On Wed, Sep 24, 2014 at 5:57 PM, Siva Dasetty wrote: > Thank you again for the reply. > > ntmpi is for threadMPI but I am using OpenMPI for MPI as I am planning to > use multiple nodes. > As I have pointed in case 7 of my post that if I use ntmpi, i get a fatal > error that says :thread mpi's are

[gmx-users] g_velacc g_dos not match!

dear all, it seems that the output of g_velacc, i.e. -o vel.xvg -os spec.xvg do not match that of g_dos, i.e. -vacf vel.xvg -dos spec.xvg, respectively, is there any reason for that? My version is 4.6.4, and I use 2 fs for time integration. Thanks, Yao -- Gromacs Users mailing list * Plea

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

Thank you again for the reply. ntmpi is for threadMPI but I am using OpenMPI for MPI as I am planning to use multiple nodes. As I have pointed in case 7 of my post that if I use ntmpi, i get a fatal error that says :thread mpi's are requested but gromacs is not compiled with thread MPI. For which

Re: [gmx-users] How can I select a group number automatically

Thank you, Erik and Chandan. They all work well. They will save me a lot of time. _ Xiaobin Cao Dept of Geology & Geophysics E235, Howe-Russell Geosciences Complex, Louisiana State University, Baton Rouge, LA 70803, U.S.A. Or redirected input: g_msd -

Re: [gmx-users] Box Vectors in .gro file

how about this one? http://en.wikipedia.org/wiki/Primitive_cell On Wed, Sep 24, 2014 at 10:53 AM, Hardy, Adam wrote: > Dear all, > > I'm trying to set up a simulation which uses a parallelepiped box. The > trouble I'm having is I don't quite understand the notation used to > describe it in the .

[gmx-users] Box Vectors in .gro file

Dear all, I'm trying to set up a simulation which uses a parallelepiped box. The trouble I'm having is I don't quite understand the notation used to describe it in the .gro file. I have read the detail here: http://manual.gromacs.org/current/online/gro.html but it's not quite enough for me. I

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

found it. http://www.gromacs.org/Documentation/Acceleration_and_parallelization GPUs are assigned to PP ranks within the same physical node in a sequential order, that is GPU 0 to the (thread-)MPI rank 0, GPU 1 to rank 1. In order to manually specify which GPU(s) to be used by mdrun, the respectiv

Re: [gmx-users] Commands to run simulations using multiple GPU's in version 5.0.1

Actually i am trying to find the answer to the same question now. manual 4.6.7/appendix D/mdrun says -gpu_id string List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping On Tue, Sep 23, 2014 at 11:07 PM, Siva Dasetty wrote: > Thank you Lu for the reply. > > As I have me

[gmx-users] error in running pdb2gmx

hi gromacs users -- 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 requests visit https://maillist.sys.kth.se/mailman/listi

Re: [gmx-users] 4.6.7 can't get regression test.

my bad, the link works. and wget it works, guess will try REGRESSIONTEST_PATH option instead. http://www.gromacs.org/Documentation/Installation_Instructions#Testing_GROMACS_for_correctness On Wed, Sep 24, 2014 at 8:52 AM, Johnny Lu wrote: > When I use cmake option "-DREGRESSIONTEST_DOWNLOAD", >

[gmx-users] 4.6.7 can't get regression test.

When I use cmake option "-DREGRESSIONTEST_DOWNLOAD", cmake gives: CMake Error at tests/CMakeLists.txt:69 (message): error: downloading 'http://gerrit.gromacs.org/download/regressiontests-4.6.7.tar.gz' failed how to fix that? -- Gromacs Users mailing list * Please search the archive at htt

[gmx-users] g_hbond -shell option

Hi, Does anyone know if the selection of atoms within the shell is updated in every frame? -- == Thomas Evangelidis PhD student University of Athens Faculty of Pharmacy Department of Pharmaceutical Chemistry Panepistimioupoli

Re: [gmx-users] which item is gpu wait for cpu?

On Wed, Sep 24, 2014 at 4:57 AM, xiexiao...@sjtu.edu.cn wrote: > I think that the items (wait GPU nonlocal) and (wait GPU local) in log file > are the time consuming that cpu wait for gpu. And Does anyone know that which > item is the time consuming that gpu wait for cpu in log file? Due to a C

Re: [gmx-users] Different energies of GPU and CPU-only runs with Gromacs 5.x

Hi, it is http://redmine.gromacs.org/issues/1603 From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [gromacs.org_gmx-users-boun...@maillist.sys.kth.se] on behalf of Johnny Lu [johnny.lu...@gmail.com] Sent: Wednesday, September 24, 2014 2:47 AM To: g

Re: [gmx-users] How can I select a group number automatically

Or redirected input: g_msd -s topol.tpr -f traj.xtc < wrote: > Use echo > > $echo 0 | g_msd -s topol.tpr -f traj.xtc > > Chandan > > On Wed, Sep 24, 2014 at 9:35 AM, Xiaobin Cao wrote: > >> Hi Gromacs users, >> >> When I do msd analysis (g_msd), there is a promotion to select a group >> num

Re: [gmx-users] (no subject)

Hi, Average structures are typically unphysical and rarely meaningful. Consider for instance the average structure of a spinning methyl group. Representative structures can be produced by clustering the frames in a trajectory and selecting the cluster centroids. See g_cluster. Kind regards, Er

[gmx-users] (no subject)

Hi GMX users what command should I use to obtain the average structure in pdb format for two nanosecond of the end of simulation.Thank you sincerely for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before post

[gmx-users] the average structure in pdb format

Hi GMX users what command should I use to obtain the average structure in pdb format for two nanosecond of the end of simulation.Thank you sincerely for your help -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before post