Dear users,
Could you please suggest me where I can get the complete package of GROMOS
54A8 force filed developed by Prof. Dr. Chris Oostenbrink and co-worker (
https://pubs.acs.org/doi/10.1021/ct300156h).
Looking forward to your suggestions.
Thanks in advance.
Sincerely yours,
Kalyanashis Jana
@email on Membrane protein Simulation:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html
Dear Najamuddin Memon
Thanks for your reply. I am a little confused here. Why is the protein
alone drifting? Typically, when we simulate protein only or protein-ligand
systems,
Hi,
I am studying self assembly of peptide monomers via MD simulation. Can
anyone suggest me regarding the calculation of aggregate size? How I can
calculate the size distribution of aggregates or oligomers..
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Pest the full error message..
On Sun 5 May, 2019, 7:59 PM Ladan Mafakhe,
wrote:
> Hello
>
> I used below command gyrate to made gyrate.xvg file
>
> gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg
> The gyrate.xvg file was generated ps time scale but I want to generate
> this curve
On 5/5/19 10:20 AM, Ladan Mafakhe wrote:
Hello
I used below command gyrate to made gyrate.xvg file
gmx gyrate -s md_0_1.tpr -f md_0_1_noPBC.xtc -o gyrate.xvg
The gyrate.xvg file was generated ps time scale but I want to generate this
curve on ns time scale . so I used below command butI
Please don't reply to the whole digest.
On 5/6/19 6:47 AM, Sankaran SV . wrote:
@email on Membrane protein Simulation:
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2019-May/125180.html
Dear Najamuddin Memon
Thanks for your reply. I am a little confused here. Why is the protein
On 5/3/19 10:20 AM, Neena Susan Eappen wrote:
Hello gromacs users,
I am interested in studying the H-bond dynamics of my protein. Do you recommend
to turn off thermostat for production run?
Why is an NVE ensemble more appropriate for what you're doing than NVT
or NPT?
-Justin
--
==
Dear users,
I've run a water membrane model through minimization, nvt, and npt with
pressure coupling = surface tension with compression 4.5e-5 4 0 and with 4.5e-5
4.5e-5. I wanted to increase the box size in the z direction to created an air
( really vacuum ) interface. The membrane is in the
Share a log file please so we can see the hardware detected, command line
options, etc.
--
Szilárd
On Sun, May 5, 2019 at 3:53 AM Maryam wrote:
> Hello Reza
> Yes I complied it with GPU and the version of CUDA is 9.1. Any suggestions?
> Thanks.
>
> On Sat., May 4, 2019, 1:45 a.m. Reza Esmaeeli,
Realise I should provide some output etc for each of these:
##
##
##
##
cmake .. -DGMX_MPI=OFF -DGMX_GPU=ON -DGMX_BUILD_MDRUN_ONLY=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs/gromas-20
-- Forwarded message -
From: ISHRAT JAHAN
Date: Tue, May 7, 2019 at 11:05 AM
Subject: atoms are not part of any of the T-Coupling groups
To:
Dear all,
I am trying to calculate the lennard Jones interaction energy between
protein and urea in the first solvation shell. I have made
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