Dear all,
I am carrying out a simulation of membrane protein with a ligand. I am
using DPPC [slipids (http://www.fos.su.se/~sasha/SLipids/Downloads.html)].
I had modified amber 03 ff by including the non-bonded and bonded
parameters from slipids website as suggested in the tutorial by Justin (
ht
Hello everyone
I did a protein water simulation. I want to calculate water density in
both interface and bulk. How can I find this resulte?
Thanks
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't po
Hi,
Thanks Mr. Bauer for your help. Actually, I was running grompp in
desktop and the mdrun in cray. Now I am running both in cray and it runs
fine.
Thanks again.
Dhrubajyoti Maji
On Mon, 10 Jun 2019 at 20:38, Paul bauer wrote:
> Hello,
>
> did you change the command to submit the calcu
Hello,
did you change the command to submit the calculation or did you use a
different machine to run the calculations?
This error usually means that the domain decomposition can't run on the
requested number of (thread)-MPI ranks.
Try using a different number of ranks or different combinatio
Hi,
You can use acpype to build the amber forcefield parameters. Each force
field have corresponding servers which can make .tpr file for you. You can
easily run simulation with that file.
On Mon 10 Jun, 2019, 6:43 PM antonia vyrkou, wrote:
> Dear all,
>
> I want to simulate an organometalli
Dear all,
I want to simulate an organometallic compound and how it affects an
enzyme's function using Gromacs but I am having trouble finding suitable
force field parameters. If would really appreciate any suggestions for a
Gromacs compatible , Amber compatible force field
Thank you
Antonia
--
gmx rdf should give you this. It will give you the radial distribution function
of the ligand molecules about the specific residue.
-Micholas
===
Micholas Dean Smith, PhD. MRSC
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Mol