On 01/27/11, Chih-Ying Lin chihying2...@gmail.com wrote:
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
On 01/27/11, bharat gupta bharat.85.m...@gmail.com wrote:
I actually don't understand exactly what u are asking .. since I am not an
expert with gromacs..
Please leave the old context for the discussion in future emails. Only you are
paying so much attention to your work that you can be
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
On 27/01/2011 7:23 PM, Chih-Ying Lin wrote:
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
Hi Camilo,
On Jan 27, 2011, at 7:19 AM, Camilo Andrés Jimenez Cruz wrote:
Sorry, abrupt sending,
the coulombtype is the same
coulombtype = cut-off
Is your cut-off actually 0.0 then?
Carsten
and constraints = all-bonds is the same. Any idea?
2011/1/27 Camilo
Dear gromacs users,
I want to ask if is it possible to amke proton proton exchange simulations
by now and constant pH simulations in new versions of Gromacs.
best,
Olga
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Please search the
Mark Abraham wrote:
On 01/27/11, *bharat gupta * bharat.85.m...@gmail.com wrote:
I actually don't understand exactly what u are asking .. since I am
not an expert with gromacs..
Please leave the old context for the discussion in future emails. Only
you are paying so much attention to
trevor brown wrote:
Dear all,
I obtained a gro file with g_x2top for a CNT.
I deleted [commands] in t and saved it as XXX.itp
What is [commands]?
Is it true? If no, how can I convert it into .itp?
A .gro file contains coordinates, while an .itp file is a topology. They're not
I generated the secondary structure profile of structure retrieved from the
last frame of the simulation ... In that profile those amino acids that are
shown as loops in VMD doesnot have any secondary structure assignment ... it
means that during simulation the structure got changed some how ...
bharat gupta wrote:
I generated the secondary structure profile of structure retrieved from
the last frame of the simulation ... In that profile those amino acids
that are shown as loops in VMD doesnot have any secondary structure
assignment ... it means that during simulation the structure
I used the same .mdp files that are given in the lysozyme tutorial .. Since
I was knowing what all parameters to change .. but after energy minimization
and equilibration steps , the graphs that I got were fine ... even the rmsd
graph of the final structure is also fine .. I have attached the
On 27/01/2011 11:11 PM, bharat gupta wrote:
I used the same .mdp files that are given in the lysozyme tutorial ..
Since I was knowing what all parameters to change .. but after energy
minimization and equilibration steps , the graphs that I got were fine
... even the rmsd graph of the final
Just I heard that molecular mechanics proton proton transfer should be soon
implemented in gromacs. That's why I am, asking it.
2011/1/27 Mark Abraham mark.abra...@anu.edu.au
On 27/01/2011 9:44 PM, Olga Ivchenko wrote:
Dear gromacs users,
I want to ask if is it possible to amke proton
Olga Ivchenko wrote:
Just I heard that molecular mechanics proton proton transfer should be
soon implemented in gromacs. That's why I am, asking it.
When a new version is released, the new features will be announced. As of right
now, these algorithms are under development and have not
On 27-01-2011 11:29, Mark Abraham wrote:
On 27/01/2011 9:44 PM, Olga Ivchenko wrote:
Dear gromacs users,
I want to ask if is it possible to amke proton proton exchange
simulations by now and constant pH simulations in new versions of Gromacs.
Not sure what you mean, but probably not. See
I don't think that there is any problem in the structure .. since I am
simulating the crystal structure taken from PDB ... and I have checked the
structure generated after pdb2gmx and solvation..
Since I am reapeating the simulation again I want to know and I am on energy
minimzation step I want
bharat gupta wrote:
I don't think that there is any problem in the structure .. since I am
simulating the crystal structure taken from PDB ... and I have checked
the structure generated after pdb2gmx and solvation..
Since I am reapeating the simulation again I want to know and I am on
Dear users,
I want to remove all waters from the xxx.pdb file. Then, I want to save the
pdb file (new pdb) without waters because I will use the methanol as a
solvent. I looked at mail list but I could not find the answer I wanted.
What should I do?
Thanks in advance
--
Ahmet YILDIRIM
--
ahmet yıldırım wrote:
Dear users,
I want to remove all waters from the xxx.pdb file. Then, I want to save
the pdb file (new pdb) without waters because I will use the methanol as
a solvent. I looked at mail list but I could not find the answer I wanted.
What should I do?
Please read
I didn't gave any -c flag while md run .. and there is no confout.gro in
my folder .. I have attached the graph obtained after energy minimzation ..
I want to ask why the graph is not coming like the one shown in the tutorial
.. I guess I asked that same question earlier also ?? .. Here is
bharat gupta wrote:
I didn't gave any -c flag while md run .. and there is no confout.gro in
my folder .. I have attached the graph obtained after energy minimzation
I've never heard of such a thing. mdrun produces several files automatically:
traj.trr, ener.edr, md.log, and confout.gro.
Hi Bharat,
If you have used the -deffnm option then the output gro will be called
whatever name you used for the -deffnm option and not the default
confout.gro.
Tom
Justin A. Lemkul wrote:
bharat gupta wrote:
I didn't gave any -c flag while md run .. and there is no confout.gro in
my
Dear All
I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.
Original messge:
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
shahid nayeem wrote:
Dear All
I am sending this mail again on user list because my reply to Mark’s
query was not uploaded on the list.
Original messge:
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
Hello,
I have a coarse-grain lipid bilayer system with a pore-forming peptide. I am
trying to use g_select to automate the detection of the opening of a water
pore.
My idea is to count the number of water molecules within a certain z
distance of the bilayer center, and flag a pore above a
Hi Xiaohu,
We are using gromacs/ORCA quite a lot. It works like any of the other
interfaced programs and whether you should use it depends on your needs
to the QM part of the QM/MM calculation.
I am using gromacs 4.0.7, but I downloaded the 4.5.3 version to test it.
I could not reproduce
Dear Gromacs Users,
I am performing an all-atom simulation of protein ligand complex in
lipid bilayer , but after around 100ns, I see that the protein started
moving in one dimension in the lipid bilayer that is it is not in the
centre, I want the position of the protein fixed through out the
Hi
On Thu, Jan 27, 2011 at 16:18, Manuel Nuno Melo m.n.m...@rug.nl wrote:
My idea is to count the number of water molecules within a certain z
distance of the bilayer center, and flag a pore above a certain threshold.
The problem is that the position of this z-slab cannot be hardcoded because
Dear GMXers,
I would like to reproduce the water droplet contact angle on graphite
surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.; Koumoutsakos, P.
*J. Phys. Chem. B* *2003*, *107*, 1345-1352.
The box size is 20nm by 20nm by 30nm. Graphite is represented by a two-layer
carbon sheet.
ram bio wrote:
Dear Gromacs Users,
I am performing an all-atom simulation of protein ligand complex in
lipid bilayer , but after around 100ns, I see that the protein started
moving in one dimension in the lipid bilayer that is it is not in the
centre, I want the position of the protein fixed
Dear Justin,
Thanks for the suggestion.
Best,
Ram
On Thu, Jan 27, 2011 at 6:46 PM, Justin A. Lemkul jalem...@vt.edu wrote:
ram bio wrote:
Dear Gromacs Users,
I am performing an all-atom simulation of protein ligand complex in
lipid bilayer , but after around 100ns, I see that the
Hey,
Well, for those things it also doesn't hurt to know a few standard linux tools:
grep -v SOL xxx.pdb nosol.pdb
And if there are also ions in play:
grep -v \(SOL\|NA\|CL\) xxx.pdb nosol.pdb
Hope it helps,
Tsjerk
2011/1/27 Justin A. Lemkul jalem...@vt.edu:
ahmet yıldırım wrote:
Dear GMX code writters,
Could anyone tell me why this comments in the code *mdlib/qmmm.c
appear*?(version 4.5.3)
at *line ~ 714*, in the beginning of subroutine* update_QMMMrec*
==
*/* updates the coordinates of both QM atoms and MM
Dear Tsjerk,
Thank you. Problem is solved.
Removing waters from the pdb file:
grep -v HOH xxx.pdb nosol.pdb
27 Ocak 2011 21:37 tarihinde Tsjerk Wassenaar tsje...@gmail.com yazdı:
Hey,
Well, for those things it also doesn't hurt to know a few standard linux
tools:
grep -v SOL xxx.pdb
Hi Gmxers,
I am just wondering if the eigenvectors in gromacs are normalized or not, and
how to check that after the normal mode analysis/
thanks,
Yao
--
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http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Hi Gmxers,
I am just wondering if the eigenvectors in gromacs are normalized or not, and
how to check that after the normal mode analysis/
thanks,
Yao
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
I am taking over a project for a graduate student who did MD using Gromacs
3.3.3. I now run similar simulations with Gromacs 4.5.1 and find that they
run only about 1/2 to 1/3 as fast as the previous runs done in Gromacs
3.3.3. The runs have about the same number of atoms and both use opls force
You will need to provide more details on the system. How many atoms,
what sort of computer system is it being run on, how many nodes, copy of
the mdp file etc.
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
381
about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a copy
of my mdp file.
title = BMIM+PF6
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 2000 ; total
Denny Frost wrote:
about 12000 atoms, 8 nodes, CentOS 5.3/Linux, infiniband. Below is a
copy of my mdp file.
title = BMIM+PF6
cpp = /lib/cpp
constraints = all_bonds
integrator = md
dt = 0.004 ; ps !
nsteps =
On 28/01/2011 4:25 AM, WU Yanbin wrote:
Dear GMXers,
I would like to reproduce the water droplet contact angle on graphite
surface, as in Werder, T.; Walther, J. H.; Halicioglu, T.;
Koumoutsakos, P. /J. Phys. Chem. B/ *2003*, /107/, 1345-1352.
The box size is 20nm by 20nm by 30nm. Graphite
On 27/01/2011 12:11 PM, Makoto Yoneya wrote:
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
In addition, you're only updating your neighbourlist every 40 ps. If
you're going to use a 4 fs timestep, I suggest that you use nstlist=5.
Also, you appear to not be using any constraints while you are using a 4
fs timestep.
I suggest that you stop worrying about why the run is slower and do
On Thu, 27 Jan 2011 19:17:18 -0500
Chris Neale chris.ne...@utoronto.ca wrote:
In addition, you're only updating your neighbourlist every 40 ps.
Surely, this should be *femto*seconds.
If you're going to use a 4 fs timestep, I suggest that you use
nstlist=5. Also, you appear to not be using
Hi Gmxers,
I am just wondering if the eigenvectors in gromacs are
normalized or not.
thanks,
Yao
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
Dear gmx-users,
My colleague seems to be experiencing an output containing errors after
issuing the command below:
mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c out -v outt.mdrun_md
The output reads as follows:
NNODES=8, MYRANK=0, HOSTNAME=node3.reyclus.loc
NODEID=0 argc=8
Justin Kat wrote:
Dear gmx-users,
My colleague seems to be experiencing an output containing errors after
issuing the command below:
mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c out -v outt.mdrun_md
The output reads as follows:
NNODES=8, MYRANK=0, HOSTNAME=node3.reyclus.loc
NODEID=0
Dear gmxusers,
I have a question here concerning nstcomm.
I got the note below after doing grompp, I'd like to do something about
it.
NOTE 1 [file HW_NPT.mdp]:
nstcomm nstcalcenergy defeats the purpose of nstcalcenergy, setting
nstcomm to nstcalcenergy
Currently, my nstcomm is
Hi all !!
Can some one clarify me what the g_mindist does. As far as I understood, it
takes two inputs from the index file. If I have more than one entry in both
of the indexes than how would g_mindist function?
eg; echo 7 8 | g_mindist -s ../md30-60.tpr -n index.ndx -f
../30-60.part0004.trr
Dear Mark and all:
Dr. Mark Abraham wrote:
So you have to update the machinery that parses the .top to recognise
that the value of 4 is now legal.
and also
Did you set the environment variable to actually call the generic
nonbonded lists?
Thanks a lot for your comments.
I did not care
Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with constraint all bonds it starts giving link
Hi Yao,
They are. But if you really want to check, convert the eigenvectors to
a human readable format (.gro/.g96) and calculate inner products :)
Cheers,
Tsjerk
On Fri, Jan 28, 2011 at 2:43 AM, Yao Yao ya...@ymail.com wrote:
Hi Gmxers,
I am just wondering if the eigenvectors in gromacs
On 28/01/2011 3:44 PM, Makoto Yoneya wrote:
Dear Mark and all:
Dr. Mark Abraham wrote:
So you have to update the machinery that parses the .top to recognise
that the value of 4 is now legal.
and also
Did you set the environment variable to actually call the generic
nonbonded lists?
Thanks a
On 28/01/2011 3:51 PM, shahid nayeem wrote:
Thanks Justin
I tried with new box size of 2.8x2.8x2.8 . During energy minimization
with steepest descent to force of 2000 and constraint=none, the system
converged in 754 steps with positive potential energy. In subsequent
simulated annealing with
Hi,
I compared the .log file time accounting for same .tpr file run alone in
serial or as part of an REMD simulation (with each replica on a single
proessor). It ran about 5-10% slower in the latter. The effect was a bit
larger when comparing the same .tpr on 8 processors with REMD with 8
Dear Mark and all:
Dr. Mark Abraham wrote:
and set the environment variable?
You'd only have learned to do this if you'd used a debugger to step
through the flow of the code. I highly recommend that procedure.
init_forcerec() checks an environment variable and triggers the use of
Dear Xiaohu,
Thanks for bringing this up. The comment has been there for ever. Since I could
not think of an application where one would not be using pbc at the time.
However, your clusters prove me wrong.
In any case, as a work-around, you may want to use a bigger box, with long
enough
Dear Gerrit,
Thanks for your comments. Strange enough, once I set up the
neighbour search from simple to grid, even the electronic embedding went
through. But I'm not sure if the calculation is right.
Generally, what happens if one is running a calculation without PBC
but the
Hi All,
I found there is a customised version gromacs-4.0.2_localpressure for
calculating the local pressure from the Gromacs website. I am wondering is
there
a higher version? The reason is that I am using CHARMM FF and have done
membrane simulations using Gromacs-4.5. If I understand
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