Re: [gmx-users] energy minimization output

2012-09-26 Thread Erik Marklund
26 sep 2012 kl. 08.16 skrev Shima Arasteh: > Dear all, > > My system contains lipids, protein and water. > I want to energy minimize it, so ran grompp: > > > # grompp -f em.mdp -c system_solv_ions.gro -p topol.top -o em.tpr > > and then: > # mdrun -v -deffnm em > > > The output is: > Steepe

Re: [gmx-users] energy minimization output

2012-09-26 Thread Archana Sonawani
Dear Erik, I also encountered similar problem. So you mean it cannot be further energy minimized? How can we proceed with NPT if the system is not in equilibrium? On Wed, Sep 26, 2012 at 1:11 PM, Erik Marklund wrote: > > 26 sep 2012 kl. 08.16 skrev Shima Arasteh: > > > Dear all, > > > > My syst

Re: [gmx-users] energy minimization output

2012-09-26 Thread Erik Marklund
It seems that your input structure has too severe clashes for energy minimization, that there are problems with your topology, or that your mdp options are not adequate. One possible solution, if your topology is correct, is to first perform an energy minimization using soft-core potentials to g

[gmx-users] g_tcaf segmentation fault

2012-09-26 Thread Stelios Karozis
Dear all, I am attempting to calculate the viscosity of a liquid binary system of 500 molecules (3050 atoms), via g_tcaf command. The system is equilibrated. The list of command I use is: /g_covar -f traj.trr -s topol.tpr -n index.ndx -o eigenval.xvg -v eigenvec.trr -av average.pdb -l covar.lo

[gmx-users] Impropers in OPLS-AA

2012-09-26 Thread Ignacio Fernández Galván
Hi all, I'm trying to build a topology file for a new molecule (benzimidazole) with the OPLS-AA force field, and I'm confused about which dihedrals and impropers I should include. I'm assuming that the molecule is similar enough to indole and adenine/guanine to use their parameters (except mayb

[gmx-users] something wrong with BlueGene/P

2012-09-26 Thread Bao Kai
Hi, all, I did many simulations with Gromacs on CO2 Water mixtures on my workstation with 8 cores in parallel, the results are pretty good. For bigger simulations, I turned to the BlueGene machine. The problem is that with exactly the same configuration files and same number of MPI tasks( 8 here)

[gmx-users] Experiences with Gromacs scaling on US supercomputer centers?

2012-09-26 Thread Michael Shirts
Hi all, I'd be interested to know about people's experiences with Gromacs on US national computing centers. Which machines have it set up to scale the best? We're putting in an XSEDE request soon, and I'm trying to figure out which resource to request. Our system is semi-coarse-grained, using r

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread lina
On Wednesday 26,September,2012 06:33 PM, Stelios Karozis wrote: > Dear all, > > I am attempting to calculate the viscosity of a liquid binary system of > 500 molecules (3050 atoms), via g_tcaf command. > The system is equilibrated. The list of command I use is: > > /g_covar -f traj.trr -s topol.t

Re: [gmx-users] Experiences with Gromacs scaling on US supercomputer centers?

2012-09-26 Thread David van der Spoel
On 2012-09-26 16:24, Michael Shirts wrote: Hi all, I'd be interested to know about people's experiences with Gromacs on US national computing centers. Which machines have it set up to scale the best? We're putting in an XSEDE request soon, and I'm trying to figure out which resource to request

[gmx-users] Re: Fast exchanges for REMD

2012-09-26 Thread Andreas Zink
Dear all, I could finally demux my REMD trajectories with high EAF. They look fine, but I'm not 100% sure about it. Unfortunately, there seems to be a "bug" in mdrun. As you migh know, the log files contain the exchange attempts like: Replica exchange at step 2000 time 4 Repl ex 012

Re: [gmx-users] Re: Fast exchanges for REMD

2012-09-26 Thread Michael Shirts
> However, the time value (4 in this example) is limited to 6 digits. Sounds like this should be increased? There's a pending change to replica exchange, so this could be added to 4.6 without disrupting the release timing. On Wed, Sep 26, 2012 at 11:22 AM, Andreas Zink wrote: > Dear all, > > I

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread Stelios Karozis
The -dt flag is the time step between the frames in ps. I tried the command in any combination i could think of. With -dt without, with -b without, and so on. The only way i get a partial result is to use the .trr file from the simulation and not from the g_covar command and even then i get the

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread lina
On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: > The -dt flag is the time step between the frames in ps. I tried the command > in any combination i could think of. With -dt without, with -b without, and > so on. The only way i get a partial result is to use the .trr file from the

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread Stelios Karozis
Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? Ο χρήστης lina έγραψε: On Thursday 27,September,2012 12:13 AM, Stelios Karozis wrote: > The -dt flag is the time step between the frames in ps. I tried the

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread lina
On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote: > Thanks for the suggestion. > I just tried and the problem presists. > Just to be clear, the right way is to use the g_covar.trr file, correct? -f traj.trr InputFull precision trajectory: trr trj cpt Here the full p

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread Justin Lemkul
On 9/26/12 12:55 PM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? The trajectory written from g_covar contains eigenvectors from PCA. I don't understand why you would use th

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread Justin Lemkul
On 9/26/12 1:12 PM, lina wrote: On Thursday 27,September,2012 12:55 AM, Stelios Karozis wrote: Thanks for the suggestion. I just tried and the problem presists. Just to be clear, the right way is to use the g_covar.trr file, correct? -f traj.trr InputFull precision trajector

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread Stelios Karozis
Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command. So the use of g_covar .trr file as an input, was easy alternative .trr file to see if i will get pass the segmantation

Re: [gmx-users] g_tcaf segmentation fault

2012-09-26 Thread Tsjerk Wassenaar
Hi Stelios, Does your .trr file contain velocities? Cheers, Tsjerk On Sep 26, 2012 8:24 PM, "Stelios Karozis" wrote: Thanks for the response. First i tried the .trr from the simulation and the result was segmentation fault. I use g_covar for entropy estimation combined with g_anaeig command.

[gmx-users] Intercalation DNA-Ethidium bromide

2012-09-26 Thread Hovakim Grabski
Dear Gromacs users, I've been running several simulations involving 26 base pairs B-DNA  and ethidium bromide. I used Autodock vina for finding inital binding sites and found one in the small groove. After that I ran a simulation of 14 ns. When I check the rmsd of Ethidium Bromide,there's a sudd

Re: [gmx-users] pca-based MD

2012-09-26 Thread James Starlight
Dear all! I've read some reference papers about EDA sampling methods and found such usefull things. First of all as I understood for biassing MD simulation along several PCs extracted from another run the make_edi -radacc 1-3 option is exactly what I need. But I havent still understood about m