Chris Neale wrote:
contrary to my previous stament, I am no longer convinced that it is
simply an initial constraints issue.
There are two things to do:
1. run gmx3.3 and gmx4.0 with the 3.3 tpr file. This should give the
same result in principle.
2. run gmx3.3 and gmx4.0 with their own tpr fi
darre...@ece.ubc.ca wrote:
Could you please let me know why GROMACS is able to find forcefields for
only 106 of the 270 atoms. My .gro file is a model of a graphene
structure with 211 equally spaced carbon atoms with the remaining
hydrogen atoms also equally spaced from the carbon atoms to which
özge kül wrote:
Hi users,
I want to plot beta factor versus residue number plot at the analyzing
part.I read manual and search in the web but I could not find a
reasonable result for this plot.I wonder if anybody know about it.
What is the beta factor?
Thank you,
Özge
Mark Abraham wrote:
geeta kant wrote:
Dear Gromacs users,
I am trying to analyze hydrogen bonding between a Protein and Drug by
g_hbond from .xtc and .tpr and .ndx files. I am getting expected
results when the H-bond donor and the hydrogen atom is from protein
while the hydrogen bond accept
Hi users,
I want to plot beta factor versus residue number plot at the analyzing part.I
read manual and search in the web but I could not find a reasonable result for
this plot.I wonder if anybody know about it.
Thank you,
Özge
___
gmx-user
Could you please let me know why GROMACS is able to find forcefields for
only 106 of the 270 atoms. My .gro file is a model of a graphene
structure with 211 equally spaced carbon atoms with the remaining
hydrogen atoms also equally spaced from the carbon atoms to which they
are bonded. Here is a s
geeta kant wrote:
Dear Gromacs users,
I am trying to analyze hydrogen bonding between a Protein and Drug by
g_hbond from .xtc and .tpr and .ndx files. I am getting expected results
when the H-bond donor and the hydrogen atom is from protein while the
hydrogen bond acceptor atom is in the dru
Dear Gromacs users,
I am trying to analyze hydrogen bonding between a Protein and Drug by
g_hbond from .xtc and .tpr and .ndx files. I am getting expected results
when the H-bond donor and the hydrogen atom is from protein while the
hydrogen bond acceptor atom is in the drug. The results are, howev
Hi,
I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2.
I have found a PDB of CA5 (PO4)3 (OH) in internet , whitch consits of 22 atoms.
the monoclinic structure of HAP has however 88 atoms and space group (P 21/b)
it means to generate the super cell of HAP i have to feed editconf with the
Hi,
I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2.
I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms.
the monoclinic structure of HAP has however 88 atoms and space group (P 21/b)
it means to generate the super cell of HAP i have to feed editconf with the
appropriate
Hi,
I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2.
I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms.
the monoclinic structure of HAP has however 88 atoms and space group (P 21/b)
it means to generate the super cell of HAP i have to feed editconf with the
appropriate
Hi,
I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2.
I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms.
the monoclinic structure of HAP has however 88 atoms and space group (P 21/b)
it means to generate the super cell of HAP i have to feed editconf with the
appropriate
Hi,
I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2.
I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms.
the monoclinic structure of HAP has however 88 atoms and space group (P 21/b)
it means to generate the super cell of HAP i have to feed editconf with the
appropriate
Hi,
I am simulating monoclinic hydroxyapatite CA10 (PO4)6 (OH)2.
I have found a PDB of CA5 (PO4)3 (OH) , whitch consits of 22 atoms.
the monoclinic structure of HAP has however 88 atoms and space group (P 21/b)
it means to generate the super cell of HAP i have to feed editconf with the
appropriate
abhigna polavarapu wrote:
Thanks Mark, thats what I really wanted to do. So can you please let
me know where I can find out the way to do position restraints and to
know how these work.
Chapter 5 in the manual, or some tutorial material (perhaps from the wiki).
Mark
___
Thanks Mark, thats what I really wanted to do. So can you please let
me know where I can find out the way to do position restraints and to
know how these work.
abhigna
On Tue, Feb 3, 2009 at 10:18 PM, Mark Abraham wrote:
> abhigna polavarapu wrote:
>>
>> Thanks David, But if I just remove the Co
abhigna polavarapu wrote:
Thanks David, But if I just remove the Copper atom and do the
simulation as copper is charged there would be sudden change in
electrostatics and the protein started unfolding when I ran the
simulation for 10ns. So I thought perturbing the charge by little
every time I ca
Thanks David, But if I just remove the Copper atom and do the
simulation as copper is charged there would be sudden change in
electrostatics and the protein started unfolding when I ran the
simulation for 10ns. So I thought perturbing the charge by little
every time I can get a structure with more
And for future reference of others, also some good data in the GROMACS 4 paper,
funny enough ;-)
GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable
Molecular Simulation
J. Chem. Theory Comput., 2008, 4 (3), pp 435447
DOI: http://dx.doi.org/10.1021/ct700301q
Catch ya,
Dall
That would be right, just find it after you sent the message.
Have found one now: http://www.hpcx.ac.uk/research/biochemistry/gromacs.html
Catch ya,
Dallas Warren
Monash University
<>___
gmx-users mailing listgmx-users@gromacs.org
http://www.gromac
Have these been done yet?
Been trying to find some, found a few individual tests, but nothing like
http://www.gromacs.org/content/view/24/37/
Catch ya,
Dallas Warren
Monash University
<>___
gmx-users mailing listgmx-users@gromacs.org
http://www.gr
Peggy Yao wrote:
Dear all,
I am new to MD simulation. I am trying to do an all-atom MD simulation
with explicit water of a protein which has a few missing side-chain
atoms of a GLN residue.
1. Which force field would you recommend? The protein is an x-ray
crystal structure, about 200 resi
Dear all,
I am new to MD simulation. I am trying to do an all-atom MD simulation with
explicit water of a protein which has a few missing side-chain atoms of a
GLN residue.
1. Which force field would you recommend? The protein is an x-ray crystal
structure, about 200 residues. Hydrogen atoms and
Perhaps this is obvious, but typically you only want to do free energy
perturbation if you are interested in computing a free energy
difference. If you are merely interested in structural properties of a
different system (in this case, the protein without the copper there)
you can simply make the c
contrary to my previous stament, I am no longer convinced that it is simply an
initial constraints issue.
In my last post, I stated: "when I define -DFLEXIBLE and make the tpr using gromacs 3 and
then run using gromacs 4, I do get gromacs 4 - identical velocities.". However, thinking more on th
maria goranovic wrote:
That sounds like a good idea. However, what sort of "cheap physical
model" are you suggesting to get rid of the very ordered initial state ?
Cut-off electrostatics with a short cut-off will be cheap and dodgy
enough for the purpose.
One could play with NPT at low press
Hi all,
Thank you for the help till now and I successfully generated the
forcefield Cu(I) binding protein. Now I wanted get the structure of non-copper
bound form which I think I can do by perturbing the charge on Cu(I) and even
perturbing the bonded and nonbonded parameters. Is there a
Thanks David, you are correct about initial step constraints. More
information inline below, but my question has been resolved.
>Chris Neale wrote:
>> Hello,
>>
>> Does anybody know if there is a reason why the .gro output velocities
>> would be different for tip4p MW in a zero-step mdrun betwee
Chris Neale wrote:
Hello,
Does anybody know if there is a reason why the .gro output velocities
would be different for tip4p MW in a zero-step mdrun between gromacs 3
and gromacs 4 (3.3.1 and 3.3.3 are the same, and are different from
4.0.2 and 4.0.3, which are themselves the same).
Is this
Hello,
Does anybody know if there is a reason why the .gro output velocities
would be different for tip4p MW in a zero-step mdrun between gromacs 3
and gromacs 4 (3.3.1 and 3.3.3 are the same, and are different from
4.0.2 and 4.0.3, which are themselves the same).
diff gmx4.0.3/feoff.gro gmx
Casey,Richard wrote:
Berk,
I'm not sure if we really need double precision. Frankly, I would rather not fool with it. However, when we run
pdb2gmx -f compound4.pdb -p compound4.top -o compound4_a.pdb
grompp -f compound4.mdp -c compound4_a.pdb -p compound4.top -o compound4.tpr
-zero
mdru
Berk,
I'm not sure if we really need double precision. Frankly, I would rather not
fool with it. However, when we run
pdb2gmx -f compound4.pdb -p compound4.top -o compound4_a.pdb
grompp -f compound4.mdp -c compound4_a.pdb -p compound4.top -o compound4.tpr
-zero
mdrun -v -s compound4.tpr -o
Hello,
I have a comment regarding the Gromacs manual. For equation (3.62) in
Chapter 3.8, \epsilon_i is called the friction constant. This is incorrect
since in that equation \epsilon is actually collision frequency and should
be represented with the letter \gamma. The product of the collision
fre
Hi,
The rpm's are only in single precision, because for nearly all purposes that
suffices
(some precision critical parts of the code are always in double precision).
Are you sure your require double precision?
If so, you will need to compile Gromacs yourself.
Berk
> From: richard.ca...@colost
Hello,
We have installed GROMACS 3.3.3 using rpm. Apparently the default installation
is single precision. We would like to use double precision. How do you run
rpm again such that it installs the double precision version of GROMACS? Not
sure what the rpm syntax would be to do this.
-
That sounds like a good idea. However, what sort of "cheap physical model"
are you suggesting to get rid of the very ordered initial state ?
-Maria
> maria goranovic wrote:
> > Hello
> >
> > I am trying to using genbox to set up a random 2-lipid mixture. Is there
> > a way to do this? First, i p
Am I wrong, or are you considering some kind of MSCG (which is not into
gromacs at least in a standard, straight forward out of the box way)? That's
nice, would be really interesting to implement, would take long time and is
still a relativelly open-field with lot to be still explored.
I think we
On Feb 3, 2009, at 4:03 PM, Elton Carvalho wrote:
On Mon, Feb 2, 2009 at 7:50 PM, XAvier Periole
wrote:
-No: is where you can find much more arguments. First of all the
two force
fields have not
been parametrized consistently. Second you'll probalby have
problems in
defining the
interac
dear Berk,
please let us know whether following patch is correct for 3.3.1
diff orig-ns.c ns.c
2c2
< * $Id: ns.c,v 1.84.2.3 2006/03/01 07:57:46 spoel Exp $
---
* $Id: ns.c,v 1.84.2.3.1 2009/02/03 20:27:00 hess Exp $
617c617
< bool bDoVdW_i,bDoCoul_i;
---
bool bDoVdW_i,bDoCo
On Mon, Feb 2, 2009 at 7:50 PM, XAvier Periole wrote:
> -No: is where you can find much more arguments. First of all the two force
> fields have not
> been parametrized consistently. Second you'll probalby have problems in
> defining the
> interactions between the two approches. How the protein wi
I'm trying to use the Buckingham potential in my simulation. First, I've
selected
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
2 2 no 0.00.0
and then in atomtype I've put A,B,C as needed by that potential.
But I have some p
maria goranovic wrote:
Hello
I am trying to using genbox to set up a random 2-lipid mixture. Is there
a way to do this? First, i put 100 POPC molecules randomly in the sim.
box. Now I want to add 28 POPS lipids. How can I do this ?
I'm not aware of a direct method for doing this. Creating in
Hello
I am trying to using genbox to set up a random 2-lipid mixture. Is there a
way to do this? First, i put 100 POPC molecules randomly in the sim. box.
Now I want to add 28 POPS lipids. How can I do this ?
thank you for helping out
-Maria
--
Maria G.
Technical University of Denmark
Copenhag
varsha gautham wrote:
Dear all,
Am trying for a simulation with polymers on a lipid bilayer.when i give
the entire polymer file which consists of 228 atoms to prodrg server for
generating itp files its taking only a block of polymer as input and
generating itp files for that polymer alone
Dear all,
Am trying for a simulation with polymers on a lipid bilayer.when i give the
entire polymer file which consists of 228 atoms to prodrg server for
generating itp files its taking only a block of polymer as input and
generating itp files for that polymer alone.I have two different monomer
Hi,
There are three ways to avoid this bug with free-energy and TIP4P:
Or make sure that any energy group that contains perturbed atoms
does not include any non-perturbed atoms with charges,
or use GMX_NO_SOLV_OPT (slow),
or use the fix below.
Berk
RCS file: /home/gmx/cvs/gmx/src/mdlib/ns.c,v
r
Sunil Thapa wrote:
Respectable Mark/David/Berk
I want to study diffusion of oxygen in water at constant pressure of 1
bar. I thus coupled my system with *berendsen* with the reference
pressureof 1 bar. But my production run gave a segmentation fault.
But when I don't couple, it doesn't. Wha
Respectable Mark/David/Berk
I want to study diffusion of oxygen in water at constant pressure of 1 bar. I
thus coupled my system with berendsen with the reference pressureof 1 bar. But
my production run gave a segmentation fault.
But when I don't couple, it doesn't. What should I do?
Your
Hi,
This Einstein method of g_energy is extremely sensitive to the system setup.
You should have perfect pressure fluctuations, which probably means shifted LJ
potential,
PME, constant volume and double precision.
Some time ago I made a comparison of different methods:
http://dx.doi.org/10.1063/
Hi,
Currently you can only get a decomposition every nstlog steps in the log file
with the mdrun option -seppot.
However, only the sum of VdW and Coulomb will be reported.
Berk
> Date: Tue, 3 Feb 2009 16:16:55 +0800
> From: friendli2...@gmail.com
> To: gmx-users@gromacs.org
> Subject: [gmx-user
Dear all,
Does Gmx provide the functions to decompose the free energy calculated
using TI into various components, such as electrostatic, VDW, covalent
or contribution from each residue?
If it has, where can I find the procedures to do it?
thanks a lot
Qiang
_
51 matches
Mail list logo