[gmx-users] How does gromacs checkpoint works

Hi all, For academic purpose, I'm wondering how does checkpoint feature in Gromacs works ? is there any resource/tutorial that I can learn ? Thank you in advance, Husen -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List

[gmx-users] restart error

Dear Grommunity, When I try and restart with the command "mpiexec -np 192 mdrun_mpi -v -deffnm md_golp_vacuo -s topol.tpr -cpi md_golp_vacuo.cpt -multidir simann59 simann60 simann61 simann62 simann63 simann64 simann65 simann66 simann67 simann68 simann69 simann70 simann71 simann72 simann73

Re: [gmx-users] least-squares fitting the second structure on the reference structure

Hi Tsjerk, Thanks, I know that. I was wondering how does a second structure (for instance third frame) fit mathematically onto the reference structure? I understand the least-square fitting for only one data set but I couldn't understand the the least-square fitting for two data sets that fit on

Re: [gmx-users] Radial Distribution Function - is there symmetry?

Thanks for the great explanation! On Wed, Jun 22, 2016 at 5:14 PM, Mark Abraham wrote: > Hi, > > In general it won't be. Take a pure NaCL cubic crystal - G(r)_NaCl is the > same as G(r)_ClNa by symmetry. Now take an identical crystal with any > single Cl replaced by

Re: [gmx-users] least-squares fitting the second structure on the reference structure

Hi Qasim, If you fit a trajectory, with trjconv -fit rot+trans, then each frame is fit onto the reference. Hope it helps, Tsjerk On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars wrote: > Dear users, > > From GROMACS online manual: > gmx confrms computes the root mean square

Re: [gmx-users] Radial Distribution Function - is there symmetry?

Hi, In general it won't be. Take a pure NaCL cubic crystal - G(r)_NaCl is the same as G(r)_ClNa by symmetry. Now take an identical crystal with any single Cl replaced by Br (or half of them, or whatever) and assume all the lattice dimensions remain the same. G(r)_ClNa is the same as before, but

[gmx-users] Radial Distribution Function - is there symmetry?

Hi, I am calculating the radial distribution function, and I am wondering if G(r)_jk = G(r)_kj. I always assumed that it was, and when I looked at the equation it seemed to be the case. But I am having trouble finding sources that state G(r)_jk = G(r)_kj, therefore I wanted to ask for your

Re: [gmx-users] selection of start or end terminus

On 6/22/16 2:19 PM, Alexander Alexander wrote: Thanks for your response. And then why does "1" go wrong for a single amino acid in zwitterions form, as well? Isn't a single amino acid is a kind of peptide with only one residue? OPLS makes special changes to CA in the case of a zwitterion.

Re: [gmx-users] selection of start or end terminus

Thanks for your response. And then why does "1" go wrong for a single amino acid in zwitterions form, as well? Isn't a single amino acid is a kind of peptide with only one residue? Thanks. Regards, Alex On Wed, Jun 22, 2016 at 8:05 PM, Justin Lemkul wrote: > > > On 6/22/16

Re: [gmx-users] selection of start or end terminus

On 6/22/16 12:53 PM, Alexander Alexander wrote: Dear Gromacs user, In the selection of start or end terminus type for peptide in OPLS_AA force field, what is the diffeece between option 0 and 1 in below list? I am interested in the Zwitterion form, but the option 0 is Zwitterion form if I am

[gmx-users] selection of start or end terminus

Dear Gromacs user, In the selection of start or end terminus type for peptide in OPLS_AA force field, what is the diffeece between option 0 and 1 in below list? I am interested in the Zwitterion form, but the option 0 is Zwitterion form if I am not wrong! Select start terminus type for 0:

Re: [gmx-users] Block averaging

Allright Sir Thank you Sent from my iPhone > On 22-Jun-2016, at 7:09 pm, Justin Lemkul wrote: > > > >> On 6/22/16 5:02 AM, sun wrote: >> Hello users and experts I have completed a 200 ns protein ligand simulation >> using GROMOS 43a1 and Gromacs v 5.0. I expected to observe

Re: [gmx-users] Job Output stops being written during long simulations on HPC cluster

Hi, Or the filesystem disappeared during the run... Mark On Wed, Jun 22, 2016 at 3:38 PM Szilárd Páll wrote: > I doubt it's a compiler issue, if anything it's more likely a > system-component that's misbehaving (kernel, or file system). I'd try > outputting to another

Re: [gmx-users] Gromacs version for polarizable model

On 6/22/16 3:11 AM, Luca Banetta wrote: Dear all, I am trying to use a polarizable model for acetone molecule. After lots of attempts we created a stable model for a single acetone molecule in a sea of water running the simulation on one core. So then we started new simulations with a certain

Re: [gmx-users] Block averaging

On 6/22/16 5:02 AM, sun wrote: Hello users and experts I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational change in protein in the presence of ligand and the results are as expected and correlates to previous

Re: [gmx-users] Gromacs tutorial similar to Justin Lemkul's

On 6/21/16 8:10 PM, Roshan Shrestha wrote: I am currently working on coarse-grain simulation of protein membrane. I am about to finish Justin Lemkul's gromacs tutorial on KALP-15 in DPPC. Are there any tutorials similar to KALP-15 or more advanced than KALP-15 which I can work on after

Re: [gmx-users] amino acid on solid surface

Hi, Why aren't you looking at distance between surface and adsorbant as a criterion? Mark On Wed, Jun 22, 2016 at 11:24 AM Alexander Alexander < alexanderwie...@gmail.com> wrote: > Dear Gromacs user, > > I am simulating the adsorption behavior of single amino acid or a short > peptide into a

[gmx-users] amino acid on solid surface

Dear Gromacs user, I am simulating the adsorption behavior of single amino acid or a short peptide into a solid surface in water, after all the minimisation, equlibrsation, and production, how should I find out if the amino acid has been absorbed? Does RMSD help? I calculated the RMSD for amino

[gmx-users] Block averaging

Hello users and experts I have completed a 200 ns protein ligand simulation using GROMOS 43a1 and Gromacs v 5.0. I expected to observe a conformational change in protein in the presence of ligand and the results are as expected and correlates to previous references as well. So, shall i believe

Re: [gmx-users] Effect of pressure coupling time constant on equilibrium densities

Hi, On Tue, Jun 21, 2016 at 4:47 PM Miguel Caro wrote: > Dear all, > > I am doing some NPT calculations for simple liquids and liquid mixtures. > I have noticed that for water I can use small time constants for the > pressure coupling (with the Berendsen barostat).

Re: [gmx-users] Dielectric Constant

Hi, On Tue, Jun 21, 2016 at 5:22 PM Life Sciences Inc < contact.lifesciences@gmail.com> wrote: > Hi > > I am getting the value of Epsilon from the output of gmx dipoles as > approximately close to 60, in my mdp file I used the default parameters for > epsilon-r (1) and for epsilon-rf(0),

Re: [gmx-users] Gromacs version for polarizable model

Hi, Don't know. Try 5.1.2. Mark On Wed, Jun 22, 2016 at 9:12 AM Luca Banetta wrote: > NNODES=1, MYRANK=0, HOSTNAME=compute-0-2.local > :-) G R O M A C S (-: > >Grunge ROck MAChoS > >

Re: [gmx-users] Gromacs version for polarizable model

NNODES=1, MYRANK=0, HOSTNAME=compute-0-2.local :-) G R O M A C S (-: Grunge ROck MAChoS :-) VERSION 4.5.4 (-: Written by Emile Apol, Rossen Apostolov, Herman J.C. Berendsen, Aldert van

[gmx-users] Gromacs version for polarizable model

Dear all, I am trying to use a polarizable model for acetone molecule. After lots of attempts we created a stable model for a single acetone molecule in a sea of water running the simulation on one core. So then we started new simulations with a certain number of acetone molecules and the

Re: [gmx-users] Does gmx covar/gmx anaeig give or T for ligand binding?

Yes, still with two ligands... So I assume that should be halved to about -0.25 kJ/mol K, which would give T= -75. I found out recently that we have access to a node with 1TB of RAM. So the solvent is still relevant? If the amount of memory I need for the entropy calculation is given by *(

Re: [gmx-users] Does gmx covar/gmx anaeig give or T for ligand binding?

On 22/06/16 06:44, Billy Williams-Noonan wrote: I re-did the calculation. When considering the entire biomolecule of each ensemble: ' = 51760 J/mol K = 50640 J/mol K = 814 J/mol K Resulting in = -0.51 kJ/mol K Still with two ligands? This still corresponds to a