Re: [gmx-users] Re: Gromacs 4.5.4 on multi-node cluster

Hi. This is openmpi related. Probably you have active the virbr0 interface with IP 192.168.122.1 on nodes. Stop and disable the libvirtd (and probably libvirt-guests) service if you don't need it. Alternatively, 1. add --mca btl_tcp_if_exclude lo,virbr0 in mpirun flags or 2. add in /home/grom

Re: [gmx-users] links warnangles

On 02/02/2011 07:47 PM, Justin A. Lemkul wrote: Dimitris Dellis wrote: Hi. There is an issue with constraints. H atom position is not uniquely defined with the constraints you use. Try these constraints (substitute symbols with numbers) 1 21 rC-H 1 31 rC-CL 1

Re: [gmx-users] links warnangles

Hi. There is an issue with constraints. H atom position is not uniquely defined with the constraints you use. Try these constraints (substitute symbols with numbers) 1 21 rC-H 1 31 rC-CL 1 41 rC-CL 1 51 rC-CL 2 31 rH-

Re: [gmx-users] Re: Problems with non-bonded interactions using OPLSAA

Hi. I found the same behavior with both 3 (3.3.3) and 4 (4.0.5) versions on x86_64. What I found is : 1. gen-pair correctly generates the 1-4 parameters (verified with gmxdump -s topol.tpr) But with no [pairs] defined, 1-4 interactions are not calculated no matter what the scale factor i

Re: [gmx-users] gromacs 3.3.3 vs 4.0.3 performance

David van der Spoel wrote: Dimitris Dellis wrote: Justin A. Lemkul wrote: Dimitris Dellis wrote: Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower

Re: [gmx-users] gromacs 3.3.3 vs 4.0.3 performance

Justin A. Lemkul wrote: Dimitris Dellis wrote: Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 (30% higher hours/ns), for few systems (512

[gmx-users] gromacs 3.3.3 vs 4.0.3 performance

Hi. I run the same (exactly) simulations with v3.3.3 and v4.0.3, on the same 64bit Q6600/DDR2-1066 machine, gcc-4.3.2 ,fftw-3.2. I found that the performance of 4.0.3 is roughly 30% lower than 3.3.3 (30% higher hours/ns), for few systems (512 molecules of 5-15 sites, nstlist=10) I tried. This

Re: [gmx-users] Equilibrating systems of rigid molecules

Hi Jussi Lehtola wrote: Hi, is it possible to simulate rigid molecules with GROMACS? Yes, rigid up to shake accuracy, but only using constraints in topol. It seems that the run option constraints = all-angles does this, but using it requires SHAKE, which cannot be used in energy m

Re: [gmx-users] FFTW & Gromacs installation on AIX 5.3

ls -l /applic/local/lib/libfftw* should see libfftw3f.a there (libfftw3.a is the double precision, libfftw3f.a is the single precision fftw3 lib) export LIBS='-L/applic/local/lib -lfftw3f' ./configure ... Senthil Kumar M wrote: > Hi, > > Earlier i had faced problems installing FFTW on IBM

[gmx-users] Planar molecules / virtual sites

Hi All, I try to simulate with gromacs substituted ethlyle series of molecules (planar) and I have to keep molecules rigid. In case of atomic substitutes, I use 3 virtual sites on the plane of molecule, that reproduce mass and moment of inertia, I use 3 constrains to keep them rigid and the mass

[gmx-users] Re: Pressure and All-bonds

rrect" temperature and almost double pressure, while in NVE, it gives almost double temperature and "correct" pressure, for my case (18 bond+angle potentials, 15 constraints needed). D. Dimitris Dellis wrote: Hi All. I try to use different potential models with an Oh symmetry m

[gmx-users] Pressure and All-bonds

Hi All. I try to use different potential models with an Oh symmetry molecule. I created a topol with nonbond_params, bonds and angles sections, no include etc. Initial configuration comes from another program that deals only rigid bodies, potential parameters come from literature, tested with o