In gromacs you can not calculate h-bond life time. You can use mdanalysis
tool for calculating h-bond lifetime.
On Tue 14 May, 2019, 11:56 AM , wrote:
> Then what is the right way to calculate lifetime of a hydrogen bond?
> - Message from Bratin Kumar Das <177cy500.bra...@nitk.edu.in>
> --
Then what is the right way to calculate lifetime of a hydrogen bond?
- 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-use
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:
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
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 edi
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 to
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 ele
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, 8:51
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
i
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 cal
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 t
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 simul
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
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
> gromacs
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 mdru
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 -
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 an
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 molecu
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 box
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 th
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