Thanks Justin,
What do you means? I have carried out gmx distance to calculate the COM
distance between two groups one by one through the previous confxxx.gro by
myself, however I never met some fail or warnings. Finally, it seems that I can
calculate the distance from all confxxx.gro as well
On 8/18/17 9:03 PM, Ming Tang wrote:
Dear Justin,
So happy to see your reply. Thanks for your explanation. The nonbonded parameters were
developed under GROMOS.ff. I actually used GROMOS.ff for my simulations, but I found
this force field is not suitable for my protein (BMP2), as it unfolded
Dear Justin,
So happy to see your reply. Thanks for your explanation. The nonbonded
parameters were developed under GROMOS.ff. I actually used GROMOS.ff for my
simulations, but I found this force field is not suitable for my protein
(BMP2), as it unfolded the alpha helix structure which did not
On 8/18/17 10:54 AM, yujie liu wrote:
Helloļ¼gromacs user
I am a novice, I met some problems when I do this tutorial to learn umbrella
sample, at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html.
I am using gromacs 5.1.4 and the summary_distances.d
On 8/18/17 3:43 AM, Ming Tang wrote:
Dear all,
I want to calculate sigma&epsilon for OPLSAA.ff from C6&C12 developed based on
GROMOS54a7.ff.
From the manual, I got the equations:
C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon
However, I found sigma and epsilon are different in OPLSAA and AM
On 8/18/17 1:13 AM, Dilip H N wrote:
Thank you sir.,
1] If so thn, is there any other possible way such that i can get a peptide
(two aminoacids linked) and thn simulate it in CHARMM FF.. ?? (or) in
alanine dipeptide case which is the residue name in the .rtp file..?? and
how can i remove the n
On 8/17/17 10:18 AM, Mateusz Marianski wrote:
Dear All,
Seems like a trivial issue, but google is not helpful here. I intend
to run simulations of (branched) carbohydrates in GROMACS 5.x.x using
CHARMM36 FF (params from
http://mackerell.umaryland.edu/charmm_ff.shtml). In principle, all
bui
On 8/17/17 9:38 AM, jay patil wrote:
Hello Experts,
What property we can calculate by providing -ix pullx.xvg through gmx WHAM
command. Like -if pullf.xvg can give PMF.
You get a PMF. There are just two different ways to get it, but that's
all gmx wham does.
Is there way to calculate di
Letting the simulation run for a bit longer, I also get LINCS warnings
after several ns. The issues seem to arise for the sugar part of the
molecule. This doesn't hugely surprise me, as this part of the ATB
topology is quite odd with the non-polar hydrogens included for the
sugar rings (unlike
I used the optimised pdb but I can't imagine it would change anything. I
also used the united-atom topology and the GROMOS 54A7 force field files
(the ones from the ATB the also include the parameters for the HS14 atom
type). I'm pretty sure (IIRC) that there aren't any force field changes
from
thanks a lot Tom,
I've used gromocs 53a6 ff, the united atom topology and the original
pdb,
do you used the same parameters?
should I use the optimised geometry file??
thank again for your precious help
Emiliano
On 2017-08-18 17:26, Thomas Piggot wrote:
Hi Emiliano,
So I had a spare 5
Hi Emiliano,
So I had a spare 5 mins and I found your molecule on the ATB:
https://atb.uq.edu.au/molecule.py?molid=223816#panel-md
Simulating one of these in water doesn't give me any problems with a 2
fs timestep, so you should check the starting structure of your system
and also your simula
Helloļ¼gromacs user
I am a novice, I met some problems when I do this tutorial to learn umbrella
sample, at
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/umbrella/05_pull.html.
I am using gromacs 5.1.4 and the summary_distances.dat file is not complete
while carrying
You shouldn't use PRODRG, well the default output at least (e.g. see
http://pubs.acs.org/doi/abs/10.1021/ci100335w).
The ATB is generally pretty good, and although it might not be perfect
here (e.g. as you have sugars in your structure which have been pretty
heavily optimised in different vari
>
> I have come across people describing RDF analysis between water and water
> and I always wonder what does it means. RDF can be done between protein and
> water to know the distribution of water around protein with default center
> of mass(My little knowledge) and what co-ordination number contr
Hi,
thank you for both your suggestions,
as Tom, I also think that the structure of the surfactant could be
modified by the presence of other surfactants in the aggregate form,
maybe it is not and only the non bonded parameters can have a role in
the formation of the aggregates (I am quite a
Hi,
On Fri, Aug 18, 2017 at 8:41 AM manindersingh rajawat <
rajawat.manindersi...@gmail.com> wrote:
> Dear all,
>
> I want extend a 100ns run to 150 ns. For this I use following commands:
>
> gmx convert-tpr -s md_100ns.tpr -extend 5 -o md_150ns.tpr
>
> gmx mdrun -v -deffnm md_150ns -c md_150
Hi,
There's not enough information for anybody to tell. Maybe you pulled too
hard, or with inappropriate settings.
Mark
On Thu, Aug 17, 2017 at 1:04 PM Alex Mathew wrote:
> Dear all,
>
> I set up a simulation box, in which protein kept at the middle and one
> water molecule around the pore reg
My CMAKE was like this:
/root/cmake-3.9.1-Linux-x86_64/bin/cmake .. -DGMX_BUILD_OWN_FFTW=ON
-DREGRESSIONTEST_DOWNLOAD=ON -DGMX_MPI=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-5.1.4
I have compiled mpich2 with --enable-shared option.
Souparno Adhikary,
CHPC Lab,
Department of Microbiology,
Unive
Hi,
On Fri, Aug 18, 2017 at 6:14 AM ZUO Taisen wrote:
> Dear Gromacs developer:
>
>There is a topology file of ethanol in the OPLS FF of the new
> version of Gromacs (Gromacs2016 please see bellow). However, I did not see
> any bond, angle or dihedral parameters. Does this means that Gr
Hi,
If libmpich.so is available after building with --enabled-shared, then the
MPI wrapper compilers should take care of this. If you want more help, we
need to at least see how you called cmake, using mpicc and mpic++, and more
information about what was wrong than "it still doesn't work." :-)
M
Hi Peter,
I'd imagine that in particular the CG angle parameters between beads may
well be different if you determined them by mapping on to a single one
of these surfactants in water, compared to mapping onto an ensemble of
structures in an aggregated state as the hydrophobic chains would try
Hi Dan
Thank you so much for you descriptive answers. I have few clarifications
that I have posted here. I will go through the papers here.
On Fri, Aug 18, 2017 at 5:01 PM, Dan Gil wrote:
> Hi Rahul,
>
> I can't find the exact papers right now, but I remember seeing some
> inconsistency in how
Hi Rahul,
I can't find the exact papers right now, but I remember seeing some
inconsistency in how people name these functions especially the radial
distribution function and pair correlation functions.
If we go far back into literature, we can see JG Kirkwood using pair
correlation functions as
Thanks Tasneem,
But later when I run the following commands on files from my backup data.
It works well
gmx convert-tpr -s md_100ns.tpr -extend 5 -o md_150ns.tpr
Reading toplogy and stuff from md_100ns.tpr
Reading file md_100ns.tpr, VERSION 5.0.2 (single precision)
Extending remaining runtime
Hi,
I was installing GROMACS-5.1.4 with MPI option in the server. It yielded
the following error,
[ 6%] Linking CXX shared library ../../lib/libgromacs_mpi.so
/usr/bin/ld: /usr/local/lib/libmpich.a(allreduce.o): relocation R_X86_64_32
against `.rodata.str1.8' can not be used when making a shared
As error says you have run previous simulation on gromacs-5.0.2 and now you
are running with gromacs 5.0.6
On 18 Aug 2017 12:11, "manindersingh rajawat" <
rajawat.manindersi...@gmail.com> wrote:
> Dear all,
>
> I want extend a 100ns run to 150 ns. For this I use following commands:
>
> gmx conver
Hi Tom,
thanks for your thoughts :)
I want to respond to your sampling argument: I figured that a surfactant
in solution is "more free" to sample conformations due to sterics than
one in an aggregated state, and that sampling would therefore be faster.
Your point of sampling the bonded conformat
Dear all,
I want to calculate sigma&epsilon for OPLSAA.ff from C6&C12 developed based on
GROMOS54a7.ff.
>From the manual, I got the equations:
C12 = Sigma^(6)*C6
C6 = 4*sigma^(6)*epsilon
However, I found sigma and epsilon are different in OPLSAA and AMBER, and that
C6&C12 from GROMOS and sig
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