Re: [gmx-users] Minimization problem

Thanks, Elton. I appreciate your answer, but my question was about the Warning error. The convergence value was set ok. The minimization do not go further because the error: *WARNING: there may be something wrong with energy file prt_cg.edr Found: step=-1, nre=36, nblock=0, time=-1. Trying to

Re: [gmx-users] Minimization problem

I have set nstenergy=100. I'm using gromacs compiled with double precision and even so, the stepsize was too small. i have faced this convergence problems earlier, and managed some solutions. I'm really wondering about the warning part, that I have never seen. -- Marcelo Depólo Polêto --

Re: [gmx-users] Minimization problem

Justin, I'm using gromacs 4.5.5 version, compiled in double precision. I tried to generate the .tpr file 3 times and got the same results. About the gmxcheck, i don't know how to use it to check my .edr file. How can I do this? -- Marcelo Depólo Polêto -- gmx-users mailing list

Re: [gmx-users] Fatal Error with AMBER03

Hi Eduardo, Some visualization softwares completes the structure, even if it's broken. I suggest you to look at the .pdb file directly in notepad and check out the composition of your HIS415. Regards -- Marcelo Depólo Polêto Molecular Animal Infectology Laboratory - LIMA Department of

Re: [gmx-users] Running Gromacs in Clusters

Hi Erik, That's good news! But i've got problems using more than one node per simulation (24 cores per node in my cluster). I don't know if it's a parallelization script problem or anything else. I'm using PBS scripts like this: *#!/bin/bash #PBS -N Gromacs #PBS -lselect=1:ncpus=24 #PBS -m ae

Re: [gmx-users] Re: Running Gromacs in Clusters

I thought that at first, but other softwares run in parallel. If there's a problem, it' s somehow in the PBS. My guess is that my PBS don't allow the LAM library see others nodes. But I have no clue where the problem could be. I've tried eliminating the node=X and got the error. I've tried use

Re: RE: [gmx-users] energy minimisation of carbon nanotubes.

I recommend use the double precision just to check the better result to your system. In my case, i've got much better results using emtol=0.004 and double precision. My system is too much unstable and i tried. I have no regrets... Marcelo Depolo Em 15/09/2012 22:11, Elie M elie.mouj

Re: [gmx-users] Ligand Internal energy

I am not from the area but I believe that a quantum approach is needed for proper validation of protein-ligand complex. Use Gromacs in order to lead you to the best frame (or pose), but calculate the energies in a quantum perspective. It probably wasn't a useful comment but i did anyway =) Good

Re: [gmx-users] Ligand Internal energy

But if you could simulate the environment just around the ligand, then you could calculate H-bond and angles energies in a quantum perspective. The limitation is the lack of integration time, but that can be avoided using a frame that corresponds to the average system pose. Or am I too wrong? --

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

Only the -ignh flag is wrong, as Justin said. Keep the rest of the command line. -- Marcelo Depólo -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before

Re: [gmx-users] adding hydrogens to protein with pdb2gmx

After doing the 'pdb2gmx', created the cell e filled with solvent, use the make_ndx to create an index of your system. One of the groups should be your residues that you want to freeze. Then, in your .mdp file, use 'freezegrps' and 'freezedim' in your recently created group. Don't forget the -n

[gmx-users] Force Field Choice

Dear all, Is there a consensus on force field choice? I read in this group, people suggesting compare experimental data and simulation data. But in case of there's none experimental data about structural data, what to do? I apologize previously the silly doubt. Best regards! -- Marcelo Depólo