Did you equilibrate the system? Typically you discard the initial values. You
discard by adding "-b 200" to the gmx energy command line call. This doesn't
include the first 200 Pico seconds in the averaging. 200 only is an example...
I prefer more.
Another point is that you don't seem to have
Den 2019-05-21 kl. 07:36, skrev Seketoulie Keretsu:
Dear Experts,
I am performing a protein-ligand stimulation in gromacs 2018. The
pressure value showed wild variation between -800 to 500 bar and
showed an average pressure value of -139 bar. The reference is 1 bar.
I have used the "lysozyme in
Dear Experts,
I am performing a protein-ligand stimulation in gromacs 2018. The
pressure value showed wild variation between -800 to 500 bar and
showed an average pressure value of -139 bar. The reference is 1 bar.
I have used the "lysozyme in water" simulation tutorial by Justin A.
Lemkul as a
Possibly
http://manual.gromacs.org/documentation/current/reference-manual/special/tabulated-interaction-functions.html
?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
Hi,
On Mon, 20 May 2019 at 19:55, Anh Vo wrote:
> Hi All,
>
> I’m currently running GROMACS to simulate a simple phospholipid bilayer
> membrane (POPC) under deformation.
>
> 1. For production step, GROMACS does not allow me to use Nose-Hoover
> barostat for pressure coupling, I can only choose
maybe I can add the following section in the itp file (only for the A and B
atom) and then vary the W(c12) factor
[ nonbond_params ]
; i j func V(c6) W(c12)
A B 1 0.22617E-02 0.74158E-06
if this is ok, it is very simple!
Can I define the func 1 for the atom A and B if for the system
Hi All,
I’m currently running GROMACS to simulate a simple phospholipid bilayer
membrane (POPC) under deformation.
1. For production step, GROMACS does not allow me to use Nose-Hoover
barostat for pressure coupling, I can only choose among Berendsen,
Parrinello-Rahman, Isotropic or MTTK options.
Thanks for your reply
On Mon 20 May, 2019, 9:24 PM David van der Spoel,
wrote:
> Den 2019-05-20 kl. 11:24, skrev Bratin Kumar Das:
> > Hi,
> > I wan to calculate the size of oligomers formed during the course of
> > simulation. Therefore I used gmx clustsize. The command I used is given
>
Hello,
if it takes this long then something is going wrong, so you don't need
to wait that long.
What happens when you build without MPI?
Cheers
Paul
On 20/05/2019 18:14, Nelson Chris AWE wrote:
Thanks Paul,
I have run the binary manually, and it's been going for over an hour now so I
Dear all,
by considering there is no response to my post, I suppose in gromacs there is
no way to solve exactly my problem.
Also if no exactly, has anyone a kind of suggestion to go in the direction of
my calcultation?
Many thanks in advance,
Anna
> Il 16 maggio 2019 alle 7.17
Thanks Paul,
I have run the binary manually, and it's been going for over an hour now so I
guess there is something wrong with it - I'll leave it running overnight and
see if it completes.
Cheers,
Chris
-Original Message-
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
On
Dear Justin,
Thanks a lot for the prompt reply.
I ran another simulation with a larger box size with and without external
electric field (field direction is Y-axis). I used anisotropic pressure
coupling for both simulations. Water box without external electric field had
fluctuation in the
Den 2019-05-20 kl. 11:24, skrev Bratin Kumar Das:
Hi,
I wan to calculate the size of oligomers formed during the course of
simulation. Therefore I used gmx clustsize. The command I used is given
below
> gmx clustsize -f md-cntr.xtc -s extend9.tpr -n protein_index.ndx -nc
no_of_clust.xvg
Hello,
from looking at the output from make check it looks like this is
harmless. The tests simply took longer than the internally set cut-off
of 30 seconds.
If you are unsure about the build, you can run the test binary manually
from the build directory with (./gmxpreprocess-test in the same
Hi All,
I've built gromacs on an Intel x86_64 server with GCC 7.2.0 and OpenMPI
When I run make check, I get a failure on test 29:
29 - GmxPreprocessTests (Timeout)
Any advice would be much appreciated.
Links to output files:
1. Build environment
On 5/17/19 6:15 AM, Rakesh Mishra wrote:
Dear Justin
After long time again I want to ask one question.
If suppose I want to repeat the same production
simulation ( final md simulation) for different seeds,
then how to do. Because as from the knowledge of
gromacs there is no manual way to put
On 5/19/19 7:11 PM, Dallas Warren wrote:
RDF ->
http://manual.gromacs.org/documentation/current/onlinehelp/gmx-rdf.html
Coordination number ->
https://en.wikibooks.org/wiki/Molecular_Simulation/Radial_Distribution_Functions
Will need to integrate the g(r) with radius, using the particle
On 5/19/19 11:32 PM, Nidhin Thomas wrote:
Hello GROMACS users,
I tried to apply a static electric field across a water box. I used
anisotropic pressure coupling. Details of the pressure coupling is given below.
pcoupl = Parrinello-Rahman
pcoupltype =
Hi Michael,
Our system of interest here is a set of small proteins with disordered regions.
The literature suggests that RE methods are not well-suited to sampling such
systems with dynamically "hot/cold" regions (and requiring more specialized
techniques such as the link below) on the one
Hi,
I wan to calculate the size of oligomers formed during the course of
simulation. Therefore I used gmx clustsize. The command I used is given
below
> gmx clustsize -f md-cntr.xtc -s extend9.tpr -n protein_index.ndx -nc
no_of_clust.xvg -ac avg_cluster_size -hc hist_clust.xvg -dt 100 -cut
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