Hi all gmx-users,
I have a water-protein simulated system. I want to calculate the
Tetrahedral order parameter. Can anybody help me regarding this issue.
On Thu, Aug 1, 2019, 00:52 David van der Spoel wrote:
> Den 2019-07-31 kl. 15:00, skrev Omkar Singh:
> > I calculated these two vectors
Hello,
I'm running into the following error when trying to pdb2gmx my PDB file.
Program gmx pdb2gmx, VERSION 5.1.4
Source code file:
/gpfs/apps/hpc.rhel7/Packages/Apps/Gromacs/5.1.4/Dist_514/gromacs-5.1.4/src/gromacs/gmxpreprocess/resall.c,
line: 645
Fatal error:
Residue 'C' not found in
Thanks for clarification.
On Thu, Aug 1, 2019 at 7:43 PM Justin Lemkul wrote:
>
>
> On 7/31/19 1:44 AM, Bratin Kumar Das wrote:
> > Hi,
> > I have some doubt regarding REMD simulation.
> > 1. In the .mdp file of each replica is it necessary to keep the
> > gen-temp constant?
> > as
Well there's your problem! Don't ignore things like this, the software is
giving you the warning for a reason.
You are going to have to go through that process again, and fix the
starting coordinate file you are using, or the processing, depending on
which atoms are the ones missing. The residue
I don't know where the non-integral charges come from. But When preparing the
gro file from the initial PDB file (a protein-DNA complex), I got a information
saying that there are 24 atoms missing in the structure, but I can't tell what
are these atoms. Could you tell me how to fix the atom
On 8/1/19 7:04 PM, Mohammed I Sorour wrote:
Hi,
that's what the ls -l prints,
ls -l
total 193120
drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff
-rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
-rw-r--r-- 1 tuf73544 chem 191 Aug 1 15:04
Hello gromacs users,
I want to thoroughly learn how OPLS parameters were found for modified
aminoacids (for instance aspartic acid versus neutral aspartic acid). I am
currently having unluck using DFT for parameterization.
Any help appreciated,
Neena
From:
>
> Hi,
that's what the ls -l prints,
>
> ls -l
> total 193120
> drwxr-xr-x 2 tuf73544 chem 4096 Jul 26 17:20 amber99sb_dyes.ff
> -rw-r--r-- 1 tuf73544 chem 61421681 Jul 31 19:56 em.gro
> -rw-r--r-- 1 tuf73544 chem 191 Aug 1 15:04 equilibration_NVT_script
> -rw-r--r-- 1 tuf73544
Hi,
We can't tell whether or what the problem is without more information.
Please upload your .log file to a file sharing service and post a link.
Mark
On Fri, 2 Aug 2019 at 01:05, Maryam wrote:
> Dear all
> I want to run a simulation of approximately 12000 atoms system in gromacs
> 2016.6 on
Hi,
What does ls -l return when run from your working directory?
Mark
On Fri, 2 Aug 2019 at 01:49, Mohammed I Sorour
wrote:
> Hello Dr. Dallas,
>
> Yes, the nvt.tpr was created and I had it in the local directory ready for
> the mdrun.
> Yes, those copy/pastes of the commands I used.
> Since
Hello Dr. Dallas,
Yes, the nvt.tpr was created and I had it in the local directory ready for
the mdrun.
Yes, those copy/pastes of the commands I used.
Since I'm kind of new to the MD simulations, so I'm sticking to that
tutorial
>From that command, was the nvt.tpr actually created? Can you see it in the
directory? What happens if you type in the files for each of the command
switches instead of using -deffnm to autocomplete them for you?
Are those copy/pastes of the commands you used?
Catch ya,
Dr. Dallas Warren
Drug
Hi Justin,
Thank you so much for your reply.
for the NVT run, I used the following commands
*gmx grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr*
which generated the nvt.tpr file and printed the following:
Ignoring obsolete mdp entry 'title'
Back Off! I just backed up mdout.mdp to
Dear all
I want to run a simulation of approximately 12000 atoms system in gromacs
2016.6 on GPU with the following machine structure:
Precision: single Memory model: 64 bit MPI library: thread_mpi OpenMP
support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: CUDA SIMD
instructions: AVX2_256
Go through the topologies, residue by residue, find where it deviates. Each
residue should sum to an integer charge.
Also look at how you generated the topology, actually steps involved, where
the coordinate files came from etc. Somewhere a choice has been made,
process performed that introduced
On 8/1/19 3:50 PM, Mohammed I Sorour wrote:
Dear Gromacs users,
I'm running MD simulation on a couple of DNA systems that only vary in
sequence. Most of the runs worked just fine, but surprisingly I have one
system that I got an error in the NVT equilibration step.
I'm following the
Dear Gromacs users,
I'm running MD simulation on a couple of DNA systems that only vary in
sequence. Most of the runs worked just fine, but surprisingly I have one
system that I got an error in the NVT equilibration step.
I'm following the
Dear Gromacs users,
I'm running MD simulation on a couple of DNA systems that only vary in
sequence. Most of the runs worked just fine, but surprisingly I have one
system that I got an error in the NVT equilibration step.
I'm following the tutorial
Hello,
I am working on a coarse-grained polymer system having various chain length
(20 & 62), dissolved in water with different counter-ion concentrations.
While equilibrating the systems I am consistently facing an error.
For chain Length 20;
Fatal error:
The X-size of the box (6.716921) times
On 7/31/19 1:44 AM, Bratin Kumar Das wrote:
Hi,
I have some doubt regarding REMD simulation.
1. In the .mdp file of each replica is it necessary to keep the
gen-temp constant?
as example: 300 k is the lowest temp of REMD simulation. Is it necessary to
keep the gen-temp=300 in each
On 7/31/19 4:20 AM, zhaox wrote:
Hi,
There are two groups in my system.When I use the pull code to pull
one group along the axis X, setting pull_coord1_geometry
=direction-periodic,I am confused with the "distance at start" and the
"reference at t=0".Could anyone can tell me how to
On 8/1/19 6:25 AM, Gselman, Larissa wrote:
Thank you for your answer! I used the Yasara -> Edit -> Clean Option and it
added atoms (1H, 2H and 3H for ASP and OXT for ASN) to my pdb file.
Nevertheless, I still get the same warnings when I try with -ignh. I cannot see
that there are other
Thank you for your answer! I used the Yasara -> Edit -> Clean Option and it
added atoms (1H, 2H and 3H for ASP and OXT for ASN) to my pdb file.
Nevertheless, I still get the same warnings when I try with -ignh. I cannot see
that there are other atoms missing?
When I try without -ignh, I even
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