Re: [gmx-users] re : heme group

Well, if you look into the .rtp files for the GROMOS force field, you'll find heme in there, but maybe not in the right form or not in the format you have in the .pdb file. Whether something is in the residue (building block) topology libaray is not prinicply related to being amino acid. As if the

Re: [gmx-users] eigenvalues

Hi Sanjay, Imagine yourself zig-zagging along a line from one place to another. If you look at you're motion (and the variance), you'll find that if you only look at blocks most of it is explained by the zig-zag and nicely periodic (no cosine content as in Berk Hess' paper). Good, you think. But

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

[gmx-users] flow control

hello I followed Karsten instructions for enabling flow control on HP procurve Gigabit switch but the cpu usages are still lower than 50%. do you have some comments for increasing cpu usages ___ gmx-users mailing list

RE: [gmx-users] Best performace with 0 core for PME calcuation

Hi, Setting -npme 2 is ridicolous. mdrun estimates the number of PME nodes by itself when you do not specify -npme. In most cases you need 1/3 or 1/4 of the nodes doing pme. The default -npme guess of mdrun is usually not bad, but might need to tuned a bit. At the end of the md.log file you find

[gmx-users] steered MD

Dear users, I would like to carry out steered molecular dyanmics simulations on one of my protein dimer. I have a few questions to learn regarding this. 1. The mdrun program needs -pn index.ndx file The way I understand is, we need to create the index file with groups (say atom1 to which the

Re: [gmx-users] Best performace with 0 core for PME calcuation

Berk Hess a écrit : Hi, Setting -npme 2 is ridicolous. mdrun estimates the number of PME nodes by itself when you do not specify -npme. In most cases you need 1/3 or 1/4 of the nodes doing pme. The default -npme guess of mdrun is usually not bad, but might need to tuned a bit. At the end of

Re: [gmx-users] Best performace with 0 core for PME calcuation

Mark Abraham a écrit : Nicolas wrote: Hello, I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't completely understand the results I obtain. The system I used is a 128 DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The size of the system is 9.6x9.6x10.1

Re: [gmx-users] Best performace with 0 core for PME calcuation

Nicolas wrote: Mark Abraham a écrit : Nicolas wrote: Hello, I'm trying to do a benchmark with Gromacs 4 on our cluster, but I don't completely understand the results I obtain. The system I used is a 128 DOPC bilayer hydrated by ~18800 SPC for a total of ~70200 atoms. The size of the system

[gmx-users] Box Exploding Error

Hello All, First, for this question I am referring to GROMACS 3.3.3. I have thoroughly read the archives for errors on why a simulation box might explode. My simulations require that I bring the N and C terminal ends of a ~20 amino acid peptide as close together as possible. To do this, I am

Re: [gmx-users] Box Exploding Error

VENKATESH HARIHARAN wrote: Hello All, First, for this question I am referring to GROMACS 3.3.3. I have thoroughly read the archives for errors on why a simulation box might explode. My simulations require that I bring the N and C terminal ends of a ~20 amino acid peptide as close

Re: [gmx-users] Box Exploding Error

VENKATESH HARIHARAN wrote: Hello All, First, for this question I am referring to GROMACS 3.3.3. I have thoroughly read the archives for errors on why a simulation box might explode. My simulations require that I bring the N and C terminal ends of a ~20 amino acid peptide as close together

[gmx-users] Box Exploding Error

I would like to thank everyone for their help. Several individuals responded to my initial post. The consensus seemed to be to use distance restraints. My question is, because distance restraints creates penalties if the distance between two atoms EXCEEDS UPPER BOUNDS, wouldn't that apply more

[gmx-users] g_rotacf, order parameter S2 problem

Dear all, I used g_rotacf to calculate the order parameter (S2, N-H bond in main chian). Thanks to Xavier Periole's advice, I make the index file and obtained some results. However, some results I got made me puzzling that the order parameter is negative! Here is one of my results: @

[gmx-users] about complexing protein and ligand

I want to know if there is any way in gromacs where i can complex a docked ligand mol2 file with the parent receptor protein. i have the mol2 file file consisting of the translated coordinates for the ligand. my desired output is one pdb file for the docked ligand-receptor complex. -- Shirin