Dear all,
I am trying to calculate heat capacity of a polymeric system (30k atoms)
using gromacs.
I tried the classical way from the fluctuation dependent properties using
"gmx energy", but the values are not matching experimental values.
I want to use "gmx dos" program, but I have some
Dear gromacs users,
A very happy new year to all of you. I an trying to simulate LiBr and
LiNO3. What will be the value of nrexcl in OPLS itp file for respective
cation and anions? I found nrexcl=1 for atomic ions in ions.itp file in
gromacs. Again in a tutorial of simulation of Choline
I guess I understand what you mean, but could you clarify it further? I
usually perform the simulations by the following process:
(1) energy minimization (EM); (2) NVT for 1 ns with heavy atom restraints;
(3) NPT for 1 ns with heavy atom restrains; (4) production simulation
without restraints.
On 1/2/20 8:25 PM, Sun Yeping wrote:
Hello Justin,
Your reply is very helpful. I can understand the first method for proving
repeatablity: use a different initial configuration. But how to set the
different initial velocities with the same initial configuration if not
using the "gen-vel"
On 1/2/20 3:02 PM, Christos Deligkaris wrote:
thank you Justin.
I saw on your umbrella sampling tutorial how to implement the restraints
using the pull code.
The protocol I used is (if I understand correctly your question): The
energy minimization reached the cutoff for maximum force 1000
Hello Justin,
Your reply is very helpful. I can understand the first method for proving
repeatablity: use a different initial configuration. But how to set the
different initial velocities with the same initial configuration if not
using the "gen-vel" option in the .mdp file for the production
On Tue, Dec 31, 2019 at 12:22 PM Justin Lemkul wrote:
>
>
> On 12/30/19 11:11 PM, sunyeping wrote:
> > Hello Justin,
> >
> > Thank you for your reply.
> >
> > If I need to prove the repeatability of a phenonmenon (such as the
> > peptide folding pathway or a conformational transition) in
> >
Hello everyone,
Before equillibriation I was trying to minimize my protein membrane system.
energyminimized.gro file when vizualized in vmd showed few lipid molecules
broken. Is it safe to use trjconv to make whole molecule after em or i can
proceed with breakage? This is the minimization.mdp
thank you Justin.
I saw on your umbrella sampling tutorial how to implement the restraints
using the pull code.
The protocol I used is (if I understand correctly your question): The
energy minimization reached the cutoff for maximum force 1000 in 346 steps.
My NVT equilibration was 50,000 steps
On 1/2/20 6:11 AM, Suvardhan Jonnalagadda wrote:
Hi,
Thanks for the reply. In the log file I could not find any 'LJ14' term, but
'LJ (SR) term is present.
My molecule has 17 atoms, and there are 1-4 interactions.
1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only
one
Hello,
we only added full detection and support for the newer Rizen chip-sets
with GROMACS 2019.5, so please try if the update to this version solves
your issue.
If not, please open an issue on redmine.gromacs.org so we can track the
problem and try to solve it.
Cheers
Paul
On 02/01/2020
Hi,
happy new year!
Now to my problem:
I use Gromacs 2019.3 and to try to run some simulations (roughly 30k
atoms per system) on my PC which has the following configuration:
CPU: Ryzen 3950X (overclocked to 4.1 GHz)
GPU #1: Nvidia RTX 2080 Ti
GPU #2: Nvidia RTX 2080 Ti
RAM: 64 GB
PSU:
Hi,
Thanks for the reply. In the log file I could not find any 'LJ14' term, but
'LJ (SR) term is present.
My molecule has 17 atoms, and there are 1-4 interactions.
1.) Is the LJ(SR) term not the same as LJ14, in my case, since I have only
one molecule?
2.) Also, how to see what 1-4 interactions
Thank you for your suggestion.
- Message from David van der Spoel -
Date: Thu, 2 Jan 2020 08:28:17 +0100
From: David van der Spoel
Reply-To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] lifetime of hydrogen bond
To: gmx-us...@gromacs.org
Den 2020-01-02 kl. 07:47,
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