[gmx-users] REMD

Hai Sir, I did an REMD simulation for an intrinsically disordered peptide.Then I extracted thousands of conformations(pdb) from trajectory. Now I want to compare experimental Chemical Shifts and NOE distance for the peptide with all these conformations.How can I do this? -- gmx-users

Re: [gmx-users] Gromacs GPU system question

Thanks Mirco, good info, your numbers look quite consistent. The only complicating factor is that your CPUs are overclocked by different amounts, which changes the relative performances somewhat compared to non-overclocked parts. However, let me list some prices to show that the top-of-the line AM

Re: [gmx-users] Re: Membrane Runs Crashing

On 6/26/13 8:39 PM, Neha wrote: Hi everybody, My runs keep crashing despite energy minimisation and fiddling around with nstlist values. I have been looking in the Gromacs manual particularly the interaction ranges in the domain decomposition section, which mentions that simulations can stop w

[gmx-users] Re: Membrane Runs Crashing

Hi everybody, My runs keep crashing despite energy minimisation and fiddling around with nstlist values. I have been looking in the Gromacs manual particularly the interaction ranges in the domain decomposition section, which mentions that simulations can stop with error messages about missing int

Re: [gmx-users] Extending Simulations

On 6/26/13 4:12 PM, HANNIBAL LECTER wrote: It is not very clear as to what you are trying to do? If you have the final coordinates and velocities from a previous simulation, I would recommend start a simulation using the .gro file and ensuring that you have gen-vel=no in the .mdp file. If you

Re: [gmx-users] Extending Simulations

It is not very clear as to what you are trying to do? If you have the final coordinates and velocities from a previous simulation, I would recommend start a simulation using the .gro file and ensuring that you have gen-vel=no in the .mdp file. If you have a well-equilibrated system, then the prope

[gmx-users] Extending Simulations

Hi everybody, I have a question that relates to reproducibility in Gromacs. If I have a .cpt file from a previous simulation and use that for two simulations using tpbconv, how similar should the temperature graphs etc be? When I use the .edr files to plot various properties, there is significant

[gmx-users] Re: 1-4 interactions free energy calculations

Thank you both, Michael and Justin, I have found more documentation and examples about expanded ensemble, so I think I want to be more documented before try it. Also, I will also follow Justin’s advice about checking the problem with my charge groups and dd before I continue with the simulations.

[gmx-users] Re: Settles vs. 3 normal constraints (energy conservation problem)

Dear Mark and Richard, Thank you so much for your help. I used shake tolerance of 1e-10 and it solved the issue. I am getting very good energy conservation. I would have never guessed that shake tolerance has such a huge impact! I also experimented LINC with the following options: constraint-al

Re: [gmx-users] g__dist calculate the distance of two residues from different loops

On 6/26/13 9:32 AM, aixintiankong wrote: Dear， when i keep the ligand in the active site, I use the g_dist calculate the distance of two residues from two different loops. i look the sticks model of the two residues by pymol and find that there is a gap between the two residue

[gmx-users] g__dist calculate the distance of two residues from different loops

Dear， when i keep the ligand in the active site, I use the g_dist calculate the distance of two residues from two different loops. i look the sticks model of the two residues by pymol and find that there is a gap between the two residues. after using g_dist calculate the distance, i

[gmx-users] Re: Tabulated Potentials

O'Neill, David wrote > Hello Users, > > Recently I have been trying to implement the use of tabulated potentials > in GROMACS to an system of argon atoms. > > I run a NVE simulation of 1000 argon atoms and then plot the potential > energy from the output. > > ar.itp : > > [ defaults ] > ; nbfun

Re: [gmx-users] AMBER to GROMACS conversion

On Tuesday, June 25, 2013 8:10 PM, Parker de Waal wrote: > Now I've been able to successfully convert the two .mol2 files into gromacs > .itp however I am unsure how to convert the .frcmod file as well.   I'm sorry, but while topolbuild does convert *.mol2 files into gromacs *.itp files with

Re: [gmx-users] Re: QM/MM simulations

On 6/26/13 7:02 AM, DavidPO wrote: Thank you! It's work. But another problem has appeared. Apparently this is some error associated with ORCA connecting: Back Off! I just backed up md.log to ./#md.log.5# Reading file topol.tpr, VERSION 4.6 (single precision) Using 1 MPI thread QM/MM calculati

[gmx-users] Re: QM/MM simulations

Thank you! It's work. But another problem has appeared. Apparently this is some error associated with ORCA connecting: Back Off! I just backed up md.log to ./#md.log.5# Reading file topol.tpr, VERSION 4.6 (single precision) Using 1 MPI thread QM/MM calculation requested. Layer 0 nr of QM atoms 3

[gmx-users] Fwd: Gromac trr analysis, wired interacation

Please keep GROMACS usage questions on the mailing list. If you need to share a file, do it via a file sharing service, rather than hoping an individual will appreciate having it in their inbox unsolicited. On point, do check out the http://www.gromacs.org/Documentation/FAQs, where a link to the s

Re: [gmx-users] Tabulated angles - how to use?

4.2.13 links table 5.5, which goes over several pages and has these details. Mark On Wed, Jun 26, 2013 at 10:36 AM, Steven Neumann wrote: > Dear Gmx Users, > > It is described how to use tabulated bonds/angles/dihedrals in 4.2.13 > manual. I wish to use tables with angles table_a1.xvg, table_a2.

[gmx-users] Tabulated angles - how to use?

Dear Gmx Users, It is described how to use tabulated bonds/angles/dihedrals in 4.2.13 manual. I wish to use tables with angles table_a1.xvg, table_a2.xvg However it is not described which function to use in [ angles ]. It is said about [ bonds ] function 8 or 9 but no angles... Can anyone te

Re: Fw: [gmx-users] ***using output of dl_poly in gromacs??***

On 2013-06-26 09:14, hamid mosaddeghi wrote: Dear David thansk for quick reply, but existed one problem, my system include metal and protein that metal not define in gromacs then writing topology is difficult, how do analysis with gromacs without write toplogy? any suggestion will be appreciated

Re: [gmx-users] Intel vs gcc compilers

>You're using a real-MPI process per core, and you have six cores per I was using the current setup, which is indeed not fully optimized, just to see how much the speed-up is between intel and gcc compiled. >processor. The recommended procedure is to map cores to OpenMP >threads, and choose th

Fw: [gmx-users] ***using output of dl_poly in gromacs??***

Dear David   thansk for quick reply, but existed one problem, my system include metal and protein that metal not define in gromacs then writing topology is   difficult, how do analysis  with gromacs without write toplogy?   any suggestion will be appreciated - Forwarded Message - From: