[gmx-users] umbrella sampling Protein_ligand complex distance calculation

Hi Initially I followed US-gromacs tuitorial of Dr. Lemkul.it works very fine. so I following the same tutorial for ligand-protein complex. I have pulled the ligand over 300ps using following MD_pull.mdp and also generated series of cordinate files (conf0.gro-conf300.gro) but problem is

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 165, Issue 42

Dear Jason, Did you try using a newer version of the GNU compilers (something from the 6.x line for example). New hardware and old compilers may result in poor performance. Cheers, Jernej > > -- > > Message: 1 > Date: Fri, 12

Re: [gmx-users] Heat capacity calculations from fluctuations and using g_dos

Dear David, Thank you for the response. I'll perform simulations as per your suggestions and see if I'll get more accurate heat capacity values. Thank you. On Thu, Jan 11, 2018 at 12:46 AM, David van der Spoel wrote: > Den 2018-01-10

[gmx-users] The official release of GROMACS 2018 ; Re: gromacs.org_gmx-users Digest, Vol 165, Issue 39

In case of Protein-ligand simulation, 1) Whether all commands used in GROMACS 5.1.4 is supported in GROMACS 2018 also ?. 2) Can I use a data file generated by Gromacs 5.1.4 in Gromacs 2018 to extend a completed protein-ligand simulation?. If yes which data file I should exactly copy to extend

[gmx-users] g_order for all-atom simulations for double bonds

Dear Gromacs users, I have a bilayer composed of lipids with two unsaturated bonds in each tail. I did my simulations in Gromacs v. 2016.3 in Charmm36FF. BUT, I am doing the analysis in Gromacs v. 2016.2. I want to calculate the order parameter for this lipid. Here is what I do: 1) I calculate

Re: [gmx-users] Worse GROMACS performance with better specs?

Dear Carsten, Look's like we're seeing the same thing here, but only when using gcc 4.5.3: Original performance (gcc 5.3.1, AVX512, no hwloc support): 49 ns/day With hwloc support: gcc 4.5.3, AVX2_256 = 67 ns/day gcc 4.5.3, AVX512 = can't compile gcc 5.3.1, AVX2_256 = 36 ns/day gcc 5.3.1,

[gmx-users] salvation free energy - gmx bar

Hello everyone, I am doing solvation free energy calculation for a small system (Thermodynamic Integration). At the analysis step, gmx bar (gmx bar -f md*.xvg -o -oi -oh), I am facing this error, which I never had before. I have all my md.xvg files. Could anyone help me with that? Here is

[gmx-users] Umbrella sampling-gmx distance

[ ZnS ] 123456789 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45.. [ Protein ] 761 762 763 764 765 766 767

Re: [gmx-users] Converting top or tpr to psf

Thanks Justin. It’s two protein chains, water and NaCl but there are virtual sites and CMAP (charmm27 ff). I generated the full topology with grompp so yes please could I try your script. Would CHARMM-GUI or VMD be able to generate the CMAP? Best wishes James > On Jan 11, 2018, at 8:08 AM,

Re: [gmx-users] Umbrella Sampling-gmx distance

On 1/11/18 9:50 AM, rose rahmani wrote: still like this You're not using the command syntax shown in the link I provided. -Justin # This file was created Thu Jan 11 09:46:46 2018 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable:

Re: [gmx-users] Umbrella Sampling-gmx distance

still like this # This file was created Thu Jan 11 09:46:46 2018 # Created by: # :-) GROMACS - gmx distance, VERSION 5.1.4 (-: # # Executable: /usr/local/gromacs/bin/gmx # Data prefix: /usr/local/gromacs # Command line: # gmx distance -n index.ndx -f conf0.gro -oxyz dist0.xvg

Re: [gmx-users] Umbrella Sampling-gmx distance

On 1/11/18 3:43 AM, rose rahmani wrote: Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp file for pulling: integrator = md dt = 0.001 nsteps

Re: [gmx-users] Converting top or tpr to psf

On 1/10/18 9:47 PM, jamesmkrie...@gmail.com wrote: Hi, Does anyone have any experience with creating a psf file from a gromacs topology? I have a collaborator who uses NAMD and they are going to analyse some of my gromacs simulations together with some of their simulations but need psf

Re: [gmx-users] dimensions of the box

On 1/10/18 12:56 PM, RAHUL SURESH wrote: Dear Justin I would like to add here something that is happening in my gromacs simulation. I am trying to extend timulation to another 50ns. commands as follows gmx convert-tpr -s alz.tpr -extend 5 -o extend.tpr gmx mdrun -v -deffnm extend

Re: [gmx-users] What is the most reliable way to run repeats for reproducibility?

On 1/10/18 9:59 AM, ZHANG Cheng wrote: Hi Mark, Thank you very much. ) For the link you provide, I think I could not manipulate most of the computer resources, as I submit my jobs to our cluster, and the jobs are distributed to different available cores randomly. ) For "random seed" of

[gmx-users] Umbrella Sampling-gmx distance

Hi i'm doing umbella sampling. whenever i use gmx distance after pulling in V.5.1.4 , i wouldn't have proper dist.xvg file.for example; this my mdp file for pulling: integrator = md dt = 0.001 nsteps = 250 nstxout = 5000