[gmx-users] Is openmp necessary?

2011-12-09 Thread Hsin-Lin Chiang
Hi, For mdrun, the option -nt means "Number of threads to start (0 is guess)". Is this option executed by openmp? I used this option every time. But today my technology stuff told me that we don't have openmp installed in our computer. It make me confused. Why can I compile and run mdrun -nt 12

Re: [gmx-users] Is openmp necessary?

2011-12-09 Thread Mark Abraham
On 9/12/2011 7:48 PM, Hsin-Lin Chiang wrote: Hi, For mdrun, the option -nt means "Number of threads to start (0 is guess)". Is this option executed by openmp? I used this option every time. But today my technology stuff told me that we don't have openmp installed in our computer. It make me

[gmx-users] Re: Is openmp necessary?

2011-12-09 Thread Hsin-Lin Chiang
Hi Mark, Thank you for your reply. I understand now. Sincerely yours, Hsin-Lin I want to calculate the diffusion coefficient of a small polypeptide with g_msd (see here http://www.gromacs.org/Documentation/How-tos/Diffusion_Constant) because of periodic boundary condition, when the peptide goe

[gmx-users] Fwd: Check for bad contacts and/or reduce the timestep

2011-12-09 Thread Mark Abraham
Hi, Please keep such discussions on the mailing list so that others can learn and contribute from the discussion and its archive. On point, this .mdp file has a feature about which I have already indicated a link that highlights its undesirability. Moreover, this .mdp file did not produce th

[gmx-users] Gromos parameters for atom type OA

2011-12-09 Thread Samuli Ollila
Dear all, I was comparing Gromos 45a3 and 53a6 force fields and I found something which I cannot understand. The atom type OA is described in ffG45a3nb.itp as: ;name at.num mass charge ptype c6 c12 OA8 0.000 0.000 A 0.0022619536 1.505529e-06

[gmx-users] Re: gmx-users Digest, Vol 92, Issue 49

2011-12-09 Thread Sławomir Stachura
Ah, OK. The commands I used were: g_msd -n POPC_index.ndx -lateral z -o POPC_150ns_CM_MSDlat.xvg -mol diffmol.xvg g_msd -n POPC_index.ndx -lateral z -o POPC_150ns_MW_MSDlat.xvg > > An HTML attachment was scrubbed... > URL: > http://lists.gromacs.org/pipermail/gmx-users/attachments/20111208/0

[gmx-users] gromacs/orca--qmmm

2011-12-09 Thread li yan
Dear Gromacs developers: I'm trying to run a QM-MM single point energy calculation on a structure (a small molecule with 50 water molecules with no pbc, no cutoff). I use orca for QM part amd gromacs for MM part. But when I run mdrun -nt 1 -s sp.tpr -c sp.gro -g sp.log, the ORCA run quickly and ter

Re: [gmx-users] Gromos parameters for atom type OA

2011-12-09 Thread Javier Cerezo
GROMOS force field builds the LJ parameters by multiplication of the square-rooted parameters per atom type (hence the SQRT(C6) and SQRT(C12) labels). In the case of the repulsion term (C12), up to three of such parameters are possible: SQRT(C12(1)) SQRT(C12(2)) SQRT(C12(3)), when combined wi

[gmx-users] Problem with GDP parameters generation

2011-12-09 Thread neeru sharma
Dear gromacs users, I have to simulate a protein-GDP complex using gromacs.As PRODRG was giving unreliable output, I generated Amber topology and coordinate files for GTP molecule. Then, I converted them into the corresponding gromacs topology (.top) and coordinate files (.gro) and generated param

[gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

2011-12-09 Thread Ruhollah Moussavi-Baygi
David, thank you for your reply. but, g_msd gives a diffusion coefficient which is one order of magnitude higher than expected for a small polypeptide (15 res long with gyration Rg ~ 0.8nm) with the same size. this is command line i used: g_msd-mpi -f md_mine_2nd.xtc -s md_mine_2nd.tpr -o msd_2

Re: [gmx-users] Problem with GDP parameters generation

2011-12-09 Thread Mark Abraham
On 10/12/2011 6:25 AM, neeru sharma wrote: Dear gromacs users, I have to simulate a protein-GDP complex using gromacs.As PRODRG was giving unreliable output, I generated Amber topology and coordinate files for GTP molecule. Then, I converted them into the corresponding gromacs topology (.top)

Re: [gmx-users] diffusion coefficient: apparently, g_msd messes up the MSD due to PBC

2011-12-09 Thread Matthew Zwier
Hi Ruhollah, A while ago on the list there was a discussion of extreme memory use and possibly-incorrect results from g_msd under some conditions. The problem could be worked around by imaging the trajectory with trjconv first to remove jumps across the box, then running g_msd on the results. Pe

Re: [gmx-users] mdrun_mpi error

2011-12-09 Thread aiswarya pawar
Hi, I tried giving this- ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450" and the configure process ran well. but when i gave make mdrun,

Re: [gmx-users] mdrun_mpi error

2011-12-09 Thread aiswarya pawar
Hi, I tried giving this- ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450" and the configure process ran well. but when i gave make mdrun,

Re: [gmx-users] mdrun_mpi error

2011-12-09 Thread Mark Abraham
On 10/12/2011 6:31 PM, aiswarya pawar wrote: Hi, I tried giving this- ./configure --prefix=/home/soft/gromacs --host=ppc --build=ppc64 --enable-mpi --with-fft=fftw3 MPICC="mpcc" CC="xlc" CFLAGS="-O3 -qarch=450d -qtune=450" CXX="mpixlC_r" CXXFLAGS="-O3 -qarch=450d -qtune=450" and the conf