Re: [gmx-users] water mediated Hbond

Hi Then what is the write way to calculate lifetime of a Hbond from gromacs? - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in> -     Date: Mon, 13 May 2019 22:24:51 +0530     From: Bratin Kumar Das <177cy500.bra...@nitk.edu.in> Reply-To: gmx-us...@gromacs.org Subject:

Re: [gmx-users] nmr distance restraints

Den 2019-05-13 kl. 18:42, skrev Eiso AB: Hi again, one more piece of info. If I move the subset of restraints that are intra-protein into a separate [ distance_restraints ] section just after inclusion of the ligand topology and run that , the dist.rest energies and violation start appearing in

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 27

Include complete details about what you have done, additions you have made to the files, the error you now obtain etc. Make it easier for people to help, provide as much information, files and output you can. That will speed things up, make it easier and more likely you'll get a reply. Did you

[gmx-users] Dihedral restraint for entire super structure

Hi I am trying to model a MOF solvation in water. I would like to treat MOF as a rigid framework. I have non-bonded parameters of MOF available from literature and bonded parameters from UFF (calculated using Avogadro) I mentioned bond and angle constraints in my mdp files and I would like

Re: [gmx-users] OPLS parameters for O2

Thanks Jochen and David, Can I have access to the itp file associated with O2 parameters used in one of these papers? i'm not sure how to work around the dummy atom, and partial charges. On Thu, May 9, 2019 at 5:42 PM Shadi Fuladi wrote: Hi, > I'm trying to test molecular oxygen diffusion in

Re: [gmx-users] water mediated Hbond

The lifetime of the h-bond can be calculated by calculating the autocorrelation of continuous h-bonds. I don't think gmx h-bond is suitable for continuous hydrogen ACF. It can give the intermittent h-bond ACF which can be helpful for calculating the structural relaxation. On Mon 13 May, 2019,

Re: [gmx-users] nmr distance restraints

Hi again, one more piece of info. If I move the subset of restraints that are intra-protein into a separate [ distance_restraints ] section just after inclusion of the ligand topology and run that , the dist.rest energies and violation start appearing in the log file - so the dist. rest. section

Re: [gmx-users] water mediated Hbond

Hii Thank you for your reply. So as u suggest I have to calculate 2 Hbond separately. But for how long that water mediated Hbond is stable; for that can I use Hbond number with time? For how many frames both the bonds appearing together. Is this right? One more thing is that I want to

Re: [gmx-users] HELP - Fatal error gmx pdb2gmx

On 5/13/19 9:33 AM, Edjan Silva wrote: HELP - Fatal error gmx pdb2gmx (Justin Lemkul) Yes. Includes residues in residuetypes.dat. however the same error remains. I can't see how that happens. Please post the full screen output of pdb2gmx from the failed command (and please don't reply to

Re: [gmx-users] water mediated Hbond

On 5/13/19 8:48 AM, Bratin Kumar Das wrote: Hi, You can make a ndx file containing the residue of interest and the SOL. In gmx h-bond command use the index file. It will give you water mediated hbond That's not what a water-mediated hydrogen bond is. That's when a water molecule

Re: [gmx-users] Restart dynamics when trr files removed

On 5/13/19 8:20 AM, CROUZY Serge 119222 wrote: Dear Gromacs users I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp

Re: [gmx-users] gromacs.org_gmx-users Digest, Vol 181, Issue 27

HELP - Fatal error gmx pdb2gmx (Justin Lemkul) Yes. Includes residues in residuetypes.dat. however the same error remains. Em sáb, 11 de mai de 2019 às 07:01, < gromacs.org_gmx-users-requ...@maillist.sys.kth.se> escreveu: > Send gromacs.org_gmx-users mailing list submissions to >

Re: [gmx-users] Restart dynamics when trr files removed

Hi, > But NO - I can't restart the simulation from 50 ns on without trr files There should be a checkpoint file called (by default) state.cpt that was generated when your 50 ns simulation finished. You can use this file to continue your run from the final state of that simulation with: gmx

[gmx-users] Restart dynamics when trr files removed

Dear Gromacs users I ran long MD simulations ( 50ns) with nstxout=5000 resulting in very large .trr files Realizing that I did not need these files (xtc enough), I removed them hoping to regenerate necessary restart files from a new gmx grompp and corrected mdp file (with nstxout=0)... But NO -

[gmx-users] nmr distance restraints

Hi, I've setup an mdrun with [ distance restraints ] but the restraints don't seem to have any effect on the simulation, so I'm wondering if there's anything i need to do to switch them on that I missed. gmx disre or gmx nmr doesn't give any info about restraints. and the .log file doesn't show

Re: [gmx-users] water mediated Hbond

Hi, You can make a ndx file containing the residue of interest and the SOL. In gmx h-bond command use the index file. It will give you water mediated hbond On Tue 7 May, 2019, 12:40 PM , wrote: > Dear all > I want to determine the water mediated hydrogen between DNA bases and > small

Re: [gmx-users] ligand in water

Hi The procedure you are following is not ok. Generate the co-ordinate file of ligand and the topology parameter file. Setup the box and add water to it. Lastly do energy minimisation. On Thu 9 May, 2019, 2:33 PM RAHUL SURESH, wrote: > Hi Users. > > I want to simulate ligand in the water

[gmx-users] Gromacs error while running energy minimization step

I got the following error while running the gromacs *NOTE: disabling dynamic load balancing as it is only supported with dynamics, not with integrator 'steep'.Using 16 MPI threadsUsing 4 OpenMP threads per tMPI threadOn host localhost.localdomain 2 GPUs auto-selected for