Re: [gmx-users] Is version 5.0 generating portable binaries?

Hi Raffaella, First: You absolutely shouldn’t remove all acceleration in cases like this - that would hit your performance by ~50%. Instead, you can pick the greatest common divisor, which is SSE4.1. Second, the segfault happens because we use a timing instruction. You can disable this by

[gmx-users] pbc

Is there any problem when we analyse the protein-ligand complex simulation withPBC problem without using -trjconv? Thank you kannan s -- 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

Re: [gmx-users] Simulate Lennard-Jones System

manual 4.1.1 (gromacs-4.5.5) On Fri, Jan 31, 2014 at 11:06 AM, Zhikun caiz...@gmail.com wrote: Dear users, I would like to simulate a Lennard-Jones system with one or two species of atoms. But my knowledge is only about Lennard-Jones 6-12 potential and I haven't figured out how to use that

Re: [gmx-users] Is version 5.0 generating portable binaries?

Note that both Opteron 2354 K10/Barcelona (http://goo.gl/6hyfO) and the Xeon 53xx / Clovertown (http://goo.gl/6hyfO) are quite old and none of them supports SSE4.1. Hence, pick SSE2 and build distributable binaries (AFAIK Clovertown does not support the rdtscp instructions). Also note that

Re: [gmx-users] pbc

Thank you for your reply Tsjerk.. I do many Trjconv -pbc mol -ur compact -center. but it doesn't help.. this is PBC. if i center protein the ligand goes other side at end of simulation. if i center ligand, then protein goes... if i center both, its trajectory is same as old one. How to overcome

Re: [gmx-users] pbc

On 1/31/14, 7:09 AM, kannan wrote: Thank you for your reply Tsjerk.. I do many Trjconv -pbc mol -ur compact -center. but it doesn't help.. this is PBC. if i center protein the ligand goes other side at end of simulation. if i center ligand, then protein goes... if i center both, its

[gmx-users] PLUMED tutorial 2014

Dear gromacs users We are pleased to inform you that we are holding a tutorial and user meeting for PLUMED, which is a small code that can be plugged into gromacs and other MD codes, from the 28th May to the 2nd June of this year in Belfast, Northern Ireland. The first three days of this

Re: [gmx-users] [gmx-developers] Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb

That's just weird. The Cuda API error detected does not sound good - perhaps it's a sing of a CUDA runtime bug? Maybe. I don't really have a known good configuration to work from, so locating the cause of error is a bit of a shot in the dark. I suggest that you try CUDA 5.0 and see if that

Re: [gmx-users] [gmx-developers] Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb

FYI: GROMACS is known to work on IVB-E + K20 hardware, so I'm still leaning toward thinking that this is either hardware or CUDA software error. On Fri, Jan 31, 2014 at 2:57 PM, AOWI (Anders Ossowicki) a...@novozymes.com wrote: That's just weird. The Cuda API error detected does not sound good -

Re: [gmx-users] [gmx-developers] Fatal error: cudaStreamSynchronize failed in cu_blockwait_nb

FYI: GROMACS is known to work on IVB-E + K20 hardware, so I'm still leaning toward thinking that this is either hardware or CUDA software error. Good to know. If we go ahead with this hardware setup, I might return. The next thing I'd have suggested is to plug the card into another machine

Re: [gmx-users] free energy calculations for reference state for constant pH MD simulations...

Thanks a lot Justin. I will try to find them and put into my .top file. From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se gromacs.org_gmx-users-boun...@maillist.sys.kth.se on behalf of Justin Lemkul jalem...@vt.edu Sent: Thursday, January 30, 2014

Re: [gmx-users] coenzyme-protein complex

Dear Justin I have a problem with centering the hetrodimer protein in the dodecahedron or octahedron box, the related commands are: 1.pdb2gmx -f A1CBIII-W3.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp -merge all -posrefc 1000 -renum 2.editconf -f conf.pdb -o boxed.pdb -c -d 1.0

Re: [gmx-users] coenzyme-protein complex

On 1/31/14, 11:53 AM, Mostafa Javaheri wrote: Dear Justin I have a problem with centering the hetrodimer protein in the dodecahedron or octahedron box, the related commands are: 1.pdb2gmx -f A1CBIII-W3.pdb -ff charmm27 -water tip3p -ignh -o conf.pdb -nochargegrp -merge all -posrefc 1000

[gmx-users] Error in minimisation

Dear GROMACS users, I am running membrane protein simulation. I have shrunk the area with the help of inflate.pl script.When I run energy minimisation I get this following error... Steepest Descents: Tolerance (Fmax) = 1.0e+03 Number of steps=

Re: [gmx-users] pbc

Thank you very much for your valuable suggestion Justin... best regards, kannan s I On Fri, Jan 31, 2014 at 6:31 PM, Justin Lemkul [via GROMACS] ml-node+s5086n5014192...@n6.nabble.com wrote: On 1/31/14, 7:09 AM, kannan wrote: Thank you for your reply Tsjerk.. I do many Trjconv -pbc