Dear all,
Does anyone have any experience with capping C-terminal amino acid
residues in the OPLS force field? What atomtypes should I use to
maintain neutrality of the system?
eg. If i have a cystine at the C-terminus residue, and I use the
following atomtypes
N opls_238 -0.5
H
Dear GMX users,
Hello, I would like to discuss the grompp message that tells the bonded
atoms oscillational period less than 10 times the time step. I am using
0.002 ps time step. The simulation was stopped because of LINCS warming.
Is it need to decrease time step at least 10 times?
Instead of t
For the error:
```
^Mstep 4400: timed with pme grid 96 96 60, coulomb cutoff 1.446: 467.9
M-cycles
^Mstep 4600: timed with pme grid 96 96 64, coulomb cutoff 1.372: 451.4
M-cycles
/var/spool/slurmd/job2321134/slurm_script: line 44: 29866 Segmentation
fault gmx mdrun -v -s $TPR -deffnm md_seed_f
Hi,
What driver version is reported in the respective log files? Does the error
persist if mdrun -notunepme is used?
Mark
On Mon., 2 Dec. 2019, 21:18 Chenou Zhang, wrote:
> Hi Gromacs developers,
>
> I'm currently running gromacs 2019.4 on our university's HPC cluster. To
> fully utilize the G
Hi Gromacs developers,
I'm currently running gromacs 2019.4 on our university's HPC cluster. To
fully utilize the GPU nodes, I followed notes on
http://manual.gromacs.org/documentation/current/user-guide/mdrun-performance.html.
And here is the command I used for my runs.
```
gmx mdrun -v -s $TPR
You also require a topology file for the toluene (.itp), include that in
the system topology file (.top):
*#include "toluene.itp"
*
Then add the molecule name and number of molecules added to the system to
the molecule section at the end of the system topology file:
[ molecules ]Toluene254
Den 2019-12-02 kl. 00:03, skrev SAKO MIRZAIE:
Hi All,
I want to simulate a polymer: protein system in a way that water solvent
will evaporated gradually. How should I do that? What parameters are needed
to be included in the mdp file.
Best
Alexandra Patriksson, Erik Marklund and David van de
Dear André,
Thank you very much for your email and hope Kalil has the script.
Best regards
On Mon, Dec 2, 2019 at 7:15 AM André Farias de Moura
wrote:
> Dear Sako,
>
> I'm ccing Kalil, who actually wrote and run the script to remove solvent
> molecules, he might still have it.
>
> regards
>
>
Hello,
I would like to obtain the time serie of the number of residues per turn with
GROMACS for a given peptide ? Is it possible to obtain this property with a
GROMACS tool ? If yes, how ?
Thank you
Stéphane
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Den 2019-12-02 kl. 17:10, skrev Mijiddorj B:
I recommend you to use (1) gmx insert-molecules tool to fill the box that
solvent molecule. For the number of molecules, you can use as much as a
higher number using -nmol option. The result tells you, how many molecules
inserted from ordered numbers.
I recommend you to use (1) gmx insert-molecules tool to fill the box that
solvent molecule. For the number of molecules, you can use as much as a
higher number using -nmol option. The result tells you, how many molecules
inserted from ordered numbers. (2) Then, you should manually edit the
topology
Dear All,
Good morning. I am doing the Protein Ligand complex simulation tutorial
from the Gromacs website. I followed the tutorial without any issue. When I
want to run the energy minimisation md, i get the error message
Fatal error:
grid cell cx -2147483648 cy -2147483648 out of range (max 24 2
Good day,
I have generated npt.tpr for my protein ligand and changed my npt.mdp file
according to the suggestions by GROMACS for using Brendsen and h-bonds for
constraints finally I encounter this NOTE which I think will cause further
problems in my md run :
NOTE 1 [file topol.top, line 18260]:
Hello,
I have downloaded the toluene pdb file and want to use it as solvent in
GROMACS rather than the water molecules. I have added toluene as a molecule
using gmx solvate -cs toluene.gro however, in the next steps, it is not
added to the topol.top file and I cannot go-ahead to the next steps of
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