GROMACS Users emailing list more appropriate for this question.
You can used editconf to translate, rotate coordinates around. So
move the 2nd one around, then copy / paste the coordinates into the
1st coordinate file, making sure adjust the atom number count and
maintain the correct header/foote
Hi,
Putting capping on the peptide/protein end affect the its polarity and you
should check how it could affect your protein structure or whether you want
it to be charged or not at the tails.
Cheers,
Armin
On Mon, Feb 12, 2018 at 9:39 PM, Negar Parvizi
wrote:
> Dear all Gromacs usersI have st
Carsten,
I was hoping yo use tune_pme to optimize a REMD job across multiple nodes,
so I think I need it compiled with MPI (please let me know if that logic is
incorrect).
I am indeed running on GPU nodes (I tested mdrun on the nodes and and there
was no issue).
Best,
Dan
On Mon, Feb 12, 2018 at
Dear GMX users
I used charmm36 force field to run MD simulation on my receptor and ligand
which has 2 phosphotyrosine groups. All of steps that I did are following as:
1) gmx pdb2gmx -f .pdb -o .gro -water tip4p -ignh -his2) gmx editconf -f .gro
-o newbox.gro -c -d 1.0 -bt dodecahedron3)gmx solv
Dear Gromacs users,
I am trying to simulate a large system (roughly 3M atoms including solvent)
on Gromacs version 4.5.5. I am having difficulty having mdrun execute
parallel calculations. I have run several variations (described below) of
attempting steepest descent minimization and the simulatio
Hi,
I'd like to ask about solvation energy given in gmx sasa (gromacs 2016)
with option:
-odg
What algorithm is used here, or rather - what values are given for area of
particular atom types? I guess there is publication behind this, but the
only mentioned in gmx sasa focus on solvation area. Is it
Dear gromacs users,
I am currently running simulations for protein-RNA complex. However i have
to include one Zn ion which is coordinated by 4 cysteine residues. when i
performed energy minimization itself zinc displaces. How can i restrain to
Zn, or to freeze Zn during simulations.
Thanks in ad
Hi,
The fix will be released in an upcoming 2016.5 patch release. (which
you can see in the redmine issue page "Target version" field BTW).
Cheers,
--
Szilárd
On Mon, Feb 12, 2018 at 2:49 PM, Akshay wrote:
> Hello All,
>
> I was running REMD simulations on Gromacs 2016.1 when my simulation cra
Hello All,
I was running REMD simulations on Gromacs 2016.1 when my simulation crashed
with the error
Assertion failed:
Condition: comm->cycl_n[ddCyclStep] > 0
When we turned on DLB, we should have measured cycles
I saw that there was a bug #2298 reported about this recently at
https://redmine.g
Hi
If I want to use gmx trjconv to recenter the protein in xtc file, the reference
(-s) .tpr should be the one I used in simulation (md.tpr) or I can use the
first one (em.tpr) without a difference?
This is because the protein has jumped after em step, and if I have to use
md.tpr as reference f
Hi Dan,
> On 11. Feb 2018, at 20:13, Daniel Kozuch wrote:
>
> Hello,
>
> I was recently trying to use the tune_pme tool with GROMACS 2018 with the
> following command:
>
> gmx tune_pme -np 84 -s my_tpr.tpr -mdrun 'gmx mdrun’
Maybe you need to compile gmx without MPI (so that gmx tune_pme
is a
On Fri, Feb 9, 2018 at 8:14 AM, RAHUL SURESH
wrote:
> Dear all
>
> I have carried out a protein ligand simulation for 50ns and performed a
> PBSA calculation for 10-20ns trajectory. I get a positive binding energy.
> How can I tackle it..?
>
> Thank you
>
>
I think you haven't received in respons
BS”D
Did you build with or without hwloc?
I did use hwloc.
—
Gromacs 2018 rc1 (using gcc 4.8.5)
—
Using AVX_256
You should be using AVX2_128 or AVX2_256 or Zen! The former will be fastest
in CPU-only runs, the latter can often be (a bit) faster in GPU acce
Dear all Gromacs users, I want to simulate prolactin receptor in a mixed
DPPC-DMPC bilayer. At first, I will insert the trans membrane part of the
protein (prolactin receptor) in the bilayer and do the necessary modifications
to the FF, according to the Justin,s membrane protein tutorial.
It sho
Dear all Gromacs usersI have started the tutorial on membrane protein, provided
by Justin ( KALP 15 in model membrane).Now I have two questions:1) Why Justin
adds the ACE and NH2 groups to the two ends of the peptide model?
The -ter option in pdb2 gmx command can add interactively the NH2 or NH3+
Hi Dr.Abraham
Thank you very much for your answer
yas I 've extacted configuration with 0.2 nm distance and when I want to
run NPT for first configuration,I gave that error.
I didn't undersatnd this mdp file for this step, I got this file from
umbrella sampling tutorial and I adjusted for my s
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