I am working on a protein consisting 2 chains. After performing regular MD
simulation and analysis the outputs, I got unexpecter rmsd, as shown in
arttached graph. What is the problem?
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Dear Emran Heshmati,
I can not see any graph? Did you attach it. Please verify.
Thank you
On Fri, Mar 27, 2020 at 6:21 PM Emran Heshmati wrote:
> I am working on a protein consisting 2 chains. After performing regular MD
> simulation and analysis the outputs, I got unexpecter rmsd, as shown in
>
Hello,
you can't attach files here on the mailing list. Please upload the file
somewhere and share a link to it.
Cheers
Paul
On 27/03/2020 10:35, Jorden Cabal wrote:
Dear Emran Heshmati,
I can not see any graph? Did you attach it. Please verify.
Thank you
On Fri, Mar 27, 2020 at 6:21 PM Em
Thanks to Paul and jorden, I repost my question:
I am working on a protein consisting 2 chains. After performing
regular MD simulation
and analysis the outputs, I got unexpecter rmsd, as seen in link below.
What is the problem??
https://www.4shared.com/photo/cYHAiZgJea/New_Doc_2020-03-27_042856.htm
On 3/27/20 11:10 AM, Emran Heshmati wrote:
Thanks to Paul and jorden, I repost my question:
I am working on a protein consisting 2 chains. After performing
regular MD simulation
and analysis the outputs, I got unexpecter rmsd, as seen in link below.
What is the problem??
https://www.4shared.co
Thank you Justin
On Fri, Mar 27, 2020, 19:47 Justin Lemkul wrote:
>
>
> On 3/27/20 11:10 AM, Emran Heshmati wrote:
> > Thanks to Paul and jorden, I repost my question:
> > I am working on a protein consisting 2 chains. After performing
> > regular MD simulation
> > and analysis the outputs, I go
Hi list, I have a working sim of the solvated SARS-CoV-2 main protease
dimer from
https://www.rcsb.org/structure/6Y84
using amber99sb-ildn and pdb2gmx-generated vsites for speed, and wanted to
proceed by adding some of the various proposed inhibitor ligands to the sim
for further workflow testing
Hi,
I use the following combination with Intel PSXE. It works and your problem
is likely related to the name of the Intel CXX compiler.
source /opt/intel/compilers_and_libraries/linux/bin/compilervars.sh intel64
source /opt/intel/impi/2018.4.274/bin64/mpivars.sh
source /opt/intel/mkl/bin/mklvars.s
Dear users,
I'm trying to optimize the execution of a system composed by 10
million atoms on a multi-GPU machine with GROMACS 2020.1.
I've followed the instructions given at
https://devblogs.nvidia.com/creating-faster-molecular-dynamics-simulations-with-gromacs-2020/
. However, when I ru
Hi Bjorn, This is still the recommended procedure. Contact me directly if you
need help with the conversion to an rtp file.Best, Christian
Original message From: Bjorn Wesen
Date: 27/03/2020 17:16 (GMT+01:00) To:
gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users]
Hi Bjorn, This is still the recommended procedure. Contact me directly if you
need help with the conversion to an rtp file.Best, Christian
Original message From: Bjorn Wesen
Date: 27/03/2020 17:16 (GMT+01:00) To:
gromacs.org_gmx-users@maillist.sys.kth.se Subject: [gmx-users]
Dear Gromacs Users,
I noticed that quite often after adding the solvent (water) to the protein,
the water
molecules fill in gaps inside the protein which are not occupied.
I am afraid that since their position may not be optimal (they actually
should not
be there), it will lead to artifacts as the
Hey y'all,
Ran some additional simulations and, unfortunately, I'm still experiencing
problems. Here's the mdp file that I used:
integrator = md
nsteps = 2000 ; 20 ns
dt = 0.001000
nstlist = 20
ns_type = g
Dear Gromacs users
I am running an MD simulation of the protein-ligand complex. At the start
of the production run, I am getting this warning. What does it mean and how
should I fix it?
*WARNING: There are no atom pairs for dispersion correction*
Thanks in advance.
Sadaf
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Gromacs Users mailin
Check the forcefield you are using is appropriate for your system or there
might be some problem with the ligand parameters.
On Tue, Mar 24, 2020 at 11:30 AM Sadaf Rani wrote:
> Dear Gromacs users
> I ran an MD simulation for 3ns and from the last coordinates started a free
> energy calculation
Hi all,
I look on google for any answers for such question in this maillist, and I
found related questions but no final answer.
I wish to compute the heat flux for my system using GK relations. I found the
gromacs extension force the calculation of the per atom stress
(http://www.mdstress.org/
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