Hello every1,
I have a question about interpretation of g_rdf.
I have generated a plot with g_rdf (with -com flag) of a nanoparticle in
water, and it shows an unstable graph (y-axis) the first picoseconds , and
then a smoothing of the curve towards the zero the more r-value on the
x-axis
Dear All and specially Dear Dr.Justin
I generated parameters for a typical ligand.
now I want to validate it.
How can I do it?
Please let me know references for doing this.
Of course I have read the article by Dr.Justin(Alzeimer),Unfortunately I
couldn't understand it completely and very good.
Is
mohsen ramezanpour wrote:
Dear All and specially Dear Dr.Justin
I generated parameters for a typical ligand.
now I want to validate it.
How can I do it?
Please let me know references for doing this.
Of course I have read the article by Dr.Justin(Alzeimer),Unfortunately I
couldn't understand
On 26/01/2011 6:15 PM, bharat gupta wrote:
Hi,
I ran a simulation of 10ns and now it has completed till 5ns .. I
want to stop it now and retrieve the trajectories without any errors..
Is it possible to do that ??
With most file systems you'd expect no problems from just copying them
to
Dear Justin
I don't want to rely on PRODRG server as others.
I want to do my work as accurate as possible.
Absolutely I read your papar and I know PRODRG present bad results for
estimating free energies.
I want to parametrize my drugs by GROMOS43A1 parameters as you said.
I know completely how to
On 26/01/2011 11:10 PM, mohsen ramezanpour wrote:
Dear Justin
I don't want to rely on PRODRG server as others.
I want to do my work as accurate as possible.
Absolutely I read your papar and I know PRODRG present bad results for
estimating free energies.
I want to parametrize my drugs by
Dear Dr Mark
Thanks for your guidances.
I am sorry for my last question.My english is not very good,I hope I could
say what was in my mind not what you read :-)
by the way,Thanks for your attention and your reply.
On Wed, Jan 26, 2011 at 3:55 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On
Hello!
I have a question concerning decorrelation/autocorrelation functions:
I studied the topic of autocorrelation function in Gromacs. For instance, I can
define any distance between different atoms of my IL over time (g_dist) as
*.xvg file. For g_analyze, I use this as input and plot the
Anna Marabotti wrote:
Dear Justin,
thanks a lot for your suggestions. I checked the first 50ns simulation
log files and in fact they start at zero and they don't say Gromacs
is using checkpoints. Therefore, I'll follow your suggestions and
discard the first 5ns simulations.
Just to be
Dear All:
I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have
reached step three, when I try to generate a trp file for DPPC only by
means of :
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
I get the following warning:
WARNING 1 [file minim.mdp]:
The
Dr. Ramón Garduño-Juárez wrote:
Dear All:
I am going through the Justin Lemku tutorial for KALP15 in DPPC. I have
reached step three, when I try to generate a trp file for DPPC only by
means of :
grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
I get the following warning:
I think this is because (if I remember correctly) in the downloaded DPPC
bilayer from Peter Tieleman's website the lipids have not been made
whole again and so are split across the periodic boundaries. If you run
a minimisation (so set -maxwarn to 1 during grompp) and re-run grompp on
the
Thank you, I have been to that page probably a good 100 times by now.
Was the 'No.' response with regards to my primary question? Or to the
one within the parentheses?
Suppose I remove my existing installation and reinstall, I am hoping
to figure out when/where exactly should I specify
./configure --enable-mpi --program-suffix=_mpi
make mdrun
make install-mdrun
make links
Sorry for the random asterisk* symbols they must have came through from some
formatting.
On Wed, Jan 26, 2011 at 12:53 PM, Justin Kat justin@mail.mcgill.cawrote:
Thank you, I have been to that page
/Support/Mailing_Lists
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On Wed, 26 Jan 2011 at 22:06:47 +0100 (CET), battis...@libero.it
battis...@libero.it wrote:
I am forwarding this to the Gromacs Users' list because that is the
appropriate place for this.
excuse me if I am writing you directly. I read on gromacs web page your
advise about the implicit water,
Dear all
I have got a problem with implicit water GBSA model.
My problem:
For my system I defined an atomtype in this way:
(I defined about 10 atoms type and for all I have got the same problem)
[ atomtypes ]
; name bond_type mass charge ptype sigma(nm)
epsilon(kj/mol)
NLAPT NC
Hi, All,
Just want to share information on this thread.
Regarding to the segmentation fault. I have found out that gromacs call
orca by write command to a buffer called buf. So for example, if the orca
path is
/usr/local/bin/orca
and the BASENAME(prefix of the *.tpr file) is
On Sat, Jan. 22, 2011 at 1:44 AM, Sweta Iyer i...@wehi.edu.au wrote:
On Thu, January 20, 2011 at 6:41PM, Sweta Iyer i...@wehi.edu.au wrote:
Hi, I am trying to generate topology files for a set of lipids with the
help of topolbuild1_3.tgz package found at the other software page of
Dear Berk and all:
I'd tried to rewrite the routine
src/gmxlib/nonbonded/nb_generic.c
to modify the LJ potential to the shifted and truncated one.
First, I'd add the new switch(ivdw) as case 4, but when I'd tried;
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
4 1
Dear All
I am trying to prepare a solvation box of chaps. After generating .itp and
.gro at ProDrg and thorough check of charges, I started with a box size of
6x6x6. Energy minimization, simulated annealing (Cooling under high pressure
and again heating at normal pressure) as well as final
Hi guys,
I created my .tpr through my own desktop (without parallel) using gromacs 4.0.7.
can i run .tpr parallelly using Gromacs 4.5.3(has parallel) in cluster
computer??
I want creat all my .tpr files in my own computer, and then run on HPC (High
performance computer).
Thanks
--
Yes. But it is better to use the same version. Otherwise you can't set all
parameters (e.g. nstcalcenergy)
Roland
2011/1/26 gromacs ptf1...@163.com
Hi guys,
I created my .tpr through my own desktop (without parallel) using gromacs
4.0.7.
can i run .tpr parallelly using Gromacs
Hi,
I did a 3ns simulation of a 236 amino acid protein (GFP, a beta barrel
protein), after checking the trajectory it seems that from the first frame
itself almost half portion of the two beta strands (159-171, 174-187) of GFP
got converted into a loop like structure .. which should not happen in
Hi all!
I am trying to run the dppc example located in
ftp://ftp.gromacs.org/pub/benchmarks/gmxbench-3.0.tar.gz, with the gpu
version of gromacs, when I run it I get
WARNING: OpenMM does not support leap-frog, will use velocity-verlet
integrator.
Sorry, abrupt sending,
the coulombtype is the same
coulombtype = cut-off
and constraints = all-bonds is the same. Any idea?
2011/1/27 Camilo Andrés Jimenez Cruz camilo.jimen...@gmail.com
Hi all!
I am trying to run the dppc example located in
On 01/27/11, bharat gupta bharat.85.m...@gmail.com wrote:
Hi,
I did a 3ns simulation of a 236 amino acid protein (GFP, a beta barrel
protein), after checking the trajectory it seems that from the first frame
itself almost half portion of the two beta strands (159-171, 174-187) of GFP
Hi Mark
Thanks.
I created a box of 6x6x6 inserting 7 molecule of chaps with genbox.Then I
solvated this box with genbox using -maxsol 500 and spc216.gro. On
visualization, at this stage itself uniform solvation did not occur and I
got water in one region and chaps molecule spread throughout box
I forgot to mention that when I prepared urea_water box then also I got
similar box of water in one region and urea in other region separated from
it. But on minimization and following simulated annealing
and equilibration I got a uniformly mixed urea water box.
Shahid Nayeem
On Thu, Jan 27, 2011
Hi
I issued pdb2gmx with G45a3 force field on the bovine carbonic
anhydrase
From the .top value, the ZN+2 is given qtot 1.233e-06 ..
2611 ZN2+257 ZN ZN 1137 2 65.37 ; qtot
1.233e-06
I am confused with the charges.
Isn't ZN+2 carrying +2 charges ??
I actually don't understand exactly what u are asking .. since I am not an
expert with gromacs..
I don't know when is was written .. Here are some lines from the log files
of simulation ...
Statistics over 151 steps using 31 frames
Energies (kJ/mol)
AngleProper Dih.
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