15 mar 2007 kl. 08.29 skrev sangeeta kundu:
Dear all,
I gave a simulation run of a protein using G43a1force field
at 523K using Berendson's Temperature coupling for 10 ns, But
three times it failed with the messege "segmentation fault" ,
without giving any other error messege. Pre
Georgios Patargias wrote:
Thanks for your reply David. I am trying to understand how
fitting but it is not very clear from the paper and g_dielectric -h.
For example, why do I get a segmentation fault when I issue:
g_dielectric -f dipcorr.xvg -epsRF 0 -ffn aexp -bfit 0 -eint 10
Read data set
Dear All,
I have performed a MD simulation of a helical peptide in a solvent box.
Now I am interested on determining the angle between the helix axis and the
side chain of some residues (defined by the vector form Cb to the terminal
heavy atom of each residue).
I am trying to do so using g_bu
gmx can not minimize the sio2 because YOU did something wrong somewhere.
(topology, infiniteness of the system, box, solvent)
Tsjerk
On 3/15/07, zzhwise1 <[EMAIL PROTECTED]> wrote:
hi all!
recently,i configuratued a sio2 base!
but when i minimized it in gmx,it was wrong! and show the follow
Dear All
I have added octanolas solvent...but now my problem is that if i take the itp
file as available on the gromacs site (which is in ffoplsaa) there are too many
warnings related to bond types and if i get an itp generated through prodrg
then it excludes the aliphatic hydrogens, while my g
15 mar 2007 kl. 10.37 skrev nur avneet:
Dear All
I have added octanolas solvent...but now my problem is that if i
take the itp file as available on the gromacs site (which is in
ffoplsaa) there are too many warnings related to bond types and if
i get an itp generated through prodrg then i
Hi Sangeeta,
It would be helpful to us if you gave more information than "I tried
to run a simulation and it crashed". What kind of protein, any
ligands/non-standard groups. Did you perform energy minimization, etc,
etc, etc... What's in the .mdp file?
Tsjerk
On 3/15/07, Erik Marklund <[EMAIL P
Hi all,
To work with PTR in gromacs I added the residue information in
ffG53a6.rtp, added the unknown atom names () to ffG53a6.atp and
added the residue name to aminoacids.dat.
this allowed me to make the topology file using pdb2gmx, create the
box and fill it with water. Now I want to
> Hi all,
>
>
> To work with PTR in gromacs I added the residue information in
> ffG53a6.rtp, added the unknown atom names () to ffG53a6.atp and
> added the residue name to aminoacids.dat.
> this allowed me to make the topology file using pdb2gmx, create the
> box and fill it with water. Now I w
> Dear all,
> I gave a simulation run of a protein using G43a1force field at
> 523K using Berendson's Temperature coupling for 10 ns, But three
> times it failed with the messege "segmentation fault" , without
> giving any other error messege. Previously I ran the simualtion of
> the same
Hi Tom,
setting rtp and atp files is not sufficient in order to make a complete
topology in GMX. You have to added also some new bonds, angles,
dihidrals etc... in ff*bon.itp ff*nb.itp. Check all of this. Look at all
the files for one force field (ffG53a6.* in the top folder). They may
contai
> Dear All
> I have added octanolas solvent...but now my problem is that if i take the
> itp file as available on the gromacs site (which is in ffoplsaa) there
> are too many warnings related to bond types and if i get an itp generated
> through prodrg then it excludes the aliphatic hydrogens, whi
Hi Justin :
how Tsjerk said me yesterday i forgot to change the number of the
atoms in the .gro file. Now i don't have this error when i run
editconfig command.
Thanks,
Maite
On 3/14/07, Justin Lemkul <[EMAIL PROTECTED]> wrote:
> Fatal error:
> Invalid line in peptide_dppc64_water.gro for a
Dir Tom,
I have a version of ffG53a6.rtp with PTR. It worked for me in
simulations, though I never rigorously checked the FF parameters, so no
warranty.
Contact me off list if you're interested.
Ran.
Tom Lenaerts wrote:
> Hi all,
>
>
> To work with PTR in gromacs I added the residue information
Dear All,
Thanks a lot to Mark,Tsjerk and Erik your promt reply.
It is a globular protein containing approximately 70
residues having crysal structure, without any
ligand,the simulation continued for 1.5 ns, & then
gave the segmentation fault, My .mdp file is given
below, I used SPC216 water and
Good problem description, but what was your command line, the
location of
these files you edited and the value of GMXRC? I'm surmising that
gromacs
isn't finding the .atp you changed.
What is the GMXRC?
Below a more complete description:
I first copied the entire top folder of gromacs t
Hi Sangeeta,
I think the problem is a lone sodium ion which is shaken vigorously
round by its private heat bath, at some point getting too intimate
with one of the water molecules around.
Never, never, NEVER give a handful of atoms, or a single atom, it's
own heat bath! Put the sodium in with th
Dear Tsjerk,
My protein had -5.99 charge , so I added 6 NA+ atoms, not a single one.
regards
Sangeeta
Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Sangeeta,
I think the problem is a lone sodium ion which is shaken vigorously
round by its private heat bath, at some point getti
> tc-grps = Protein SOL NA+
> tau_t = 0.1 0.1 0.1
> ref_t = 523 523 523
This is a bad idea and we see it regularly on this mailing list. Coupling
a single atom to a thermal bath is asking for trouble... what is the
temperature of a single
15 mar 2007 kl. 14.30 skrev sangeeta kundu:
Dear Tsjerk,
My protein had -5.99 charge , so I added 6 NA+ atoms, not a
single one.
Nevertheless, 6 atoms is a very small tc-group. Large fluctuations in
kinetic energy is expected for such a small collection of atoms,
making the temper
Hi Sangeeta, Mark,
Well, one, six, that's about the same thing (the same order of
magnitude at least). Maybe just over a handful, but all six of them
will be jostled around quite a bit by coupling to their private
jacuzzi!
I think a warning is a good idea, but maybe 10 is even on the low side
fo
> I think a warning is a good idea, but maybe 10 is even on the low side
> for that. Since temperature is macroscopic, you'll need enough atoms
> not to deviate too much from the target temperature. I have no
> evidence on which I can make a proper suggestion... My bidding will be
> 50! Going once
> I think a warning is a good idea, but maybe 10 is even on the low side
> for that. Since temperature is macroscopic, you'll need enough atoms
> not to deviate too much from the target temperature. I have no
> evidence on which I can make a proper suggestion... My bidding will be
> 50! Going once
Hello:
anybody know`s how to calculate the "mean life time" of solvent
arround solute? and "mean life time" of hydrogen bond ?
Thanks
silvina.
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Hello All,
Myself Sunita Gupta,I am undergoing a project right now,which is related to
"Coarse Grain Simulation".I am using Gromacs for that,
I've creatad .top and .gro file,But I am facing some problem in making .mdp
file.
Can I get any sample of .mdp file that can be used for coarse graining.
An
Hi,
Related items could be parameters for vdw, electrostatic and timesteps.
For Vdw, how much cut-off would you need? For electrostatic, what method
would you use? Cut-off (then you need to specify again how much cut-off
length) or PME (how much real space length). Timestep shall be derived
b
Tom Lenaerts wrote:
Good problem description, but what was your command line, the
location of
these files you edited and the value of GMXRC? I'm surmising that
gromacs
isn't finding the .atp you changed.
What is the GMXRC?
Below a more complete description:
I first copied the entire to
g_hbond -ac
15 mar 2007 kl. 14.52 skrev [EMAIL PROTECTED]:
Hello:
anybody know`s how to calculate the "mean life time" of solvent
arround solute? and "mean life time" of hydrogen bond ?
Thanks
silvina.
___
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I made an index file that contained the middle portion of the DNA
strand. I then used the -center option to center this middle portion
in the box and then outputted the entire molecule. However, the
molecule still appears broken. What is this -pbc mol option? That
doesn't seem to be one of the ava
Hi Robert,
Maybe it's a bit nasty, but you may try the following, assuming that
your ends stay a bit together:
1. Translate your system such that the last atom of chain A is
centered in the _rectangular_ unitcell.
2. Generate a .tpr file from the translated system
3. Convert the .tpr to .pdb
Gr
Thanks for Tsjerk's input. Rob, please make sure that that portion of
DNA is always binding together. Since you have a ssDNA, just center the
center residue.
mol was a non-existing option. It sounds meaningful =) Just use whole,
please.
Regards,
Yang Ye
Tsjerk Wassenaar wrote:
Hi Robert,
Ma
Thank Erick
My problem is actually of interpretation. I have done to simulation of two
monomers of the acid pectic in water, 10ns. When I calculate the time of
average life of the bridge between one O of a monomer with a H of another
monomer, it he goes out for me, for example, 52ps.
What it mean
May not be a residue, just pick an atom in the center residue.
Have a try and hope you succeed.
Yang Ye
Thanks for Tsjerk's input. Rob, please make sure that that portion of
DNA is always binding together. Since you have a ssDNA, just center the
center residue.
mol was a non-existing option. It s
Hello:
I have another problem. With g_hbond -ins I inserted to the dimer that I
am studying 20 water molecules to see the Hbond. Is result the same if I
insert 20, 40 or 1000 water molecules, why what I ask?. Does program count
the insertions always between the same acceptor-donor couple?. How is
Hello,
I am trying to figure out what the difference between these two
applications is. The calculation is of the RMSD for a protein unfolding
trajectory and I get different results with g_rms and g_rmsdist. I have
looked at the manual and all I can find is that:
"g_rmsdist computes the root
Is there any way to remultiplex a REMD trajectory? If so, this chain
of events should work:
1. Demultiplex the REMD trajectory (with demux.pl) to obtain a
continuous trajectory
2. Use trjconv -pbc nojump on the demultiplexed trajectories
3. Remultiplexed the "nojumped" trajectories back
I tried
>Not only in atp, but also in bon and nb. nb is a bit easy, only LJ
>parameters. But for bon, you need to specify any bonded, angle, dihedral
>interaction that CB and CR61 have in your molecule.
The structure of these files is completely unclear to me. I also didn't find
any explanation of the
>Not only in atp, but also in bon and nb. nb is a bit easy, only LJ
>parameters. But for bon, you need to specify any bonded, angle, dihedral
>interaction that CB and CR61 have in your molecule.
The structure of these files is completely unclear to me. I also didn't find
any explanation of the
Hi Gleb,
g_rmsdist calculates a matrix of interatomic distances, averages these
and calculates the average deviation from the average. g_rms
superimposes two structures (superimposes the averages) and calculates
the average deviation over the pairs of equal atoms in the structures.
Hope I am cle
Tom Lenaerts wrote:
Not only in atp, but also in bon and nb. nb is a bit easy, only LJ
parameters. But for bon, you need to specify any bonded, angle, dihedral
interaction that CB and CR61 have in your molecule.
The structure of these files is completely unclear to me. I also didn't find
any
Tom,
Now before anything else..., do you need a CB to be defined? Doesn't
one of the atom types present suffice? There's tyrosine in most force
field already, you know, and these 'CB' atoms are merely part of the
ring.
Tsjerk
On 3/15/07, David van der Spoel <[EMAIL PROTECTED]> wrote:
Tom Lenae
Hello everyone,
As I was discussing in a previous thread, I'm having problems
visualizing/analyzing an REMD trajectory of ssDNA. As I understand,
most tools for unwrapping PBC (i.e. removing the jumps from one side
of the box to the other) do so by detecting large displacements
between successive
>Tom,
>
>Now before anything else..., do you need a CB to be defined? Doesn't
>one of the atom types present suffice? There's tyrosine in most force
>field already, you know, and these 'CB' atoms are merely part of the
>ring.
Indeed. If I just replace the CB and CR61 by C in the rtp file
and add
> Indeed. If I just replace the CB and CR61 by C in the rtp file
> and add the bondtypes using the G53a6bon.itp then PTR is defined as
> follows
Presumably you've checked some useful source that this carbon atom type is
reasonable to use for a tyrosine ring.
> WARNING 1 [file "sh2_pep.top", lin
Hi Bob,
This would give an intolerable decrease in performance, because of the
neighbour searching thing.
I had a routine which might be of help, but unfortunately somewhere in
the process of "improvement" I broke it and didn't return to it again.
Maybe I can have a look at it some moment these
> Thank Erick
>
> My problem is actually of interpretation. I have done to simulation of two
> monomers of the acid pectic in water, 10ns. When I calculate the time of
> average life of the bridge between one O of a monomer with a H of another
> monomer, it he goes out for me, for example, 52ps.
>
If you're not planning on running parallel jobs I would go for the
higher clock speed. If you're running parallel, well, I am not sure.
On 3/13/07, Andrei Neamtu <[EMAIL PROTECTED]> wrote:
Hello,
We are in the process of building a cluster on which GROMACS will be
the main computational engine
Hello everyone,
Can anyone tell me or post me publication or link which contains information
how GROMOS force field differs from Amber ff.
regards,
Michal W.
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Dear gmx users,
I have a question about g_mdmat, related to a question I posed earlier. I know
a bit more now. When I run the command on a trajectory in pdb format, either
using -b and -e to specify which string of frames to average over, or just
leaving -b, -e unspecified, I get a contact ma
Hi all,
I am struggling with the rdf. I have 7 structural ions in my protein and
I'd like to monitor the coordination number around them (ion - protein)
during my MD. I have read papers about it and:
http://www.gromacs.org/pipermail/gmx-users/2006-November/024911.html
and
http://www.gromacs.org/pip
Dear users:
I have a position restrain .mdp file need to set,I use 300K
in which an isotropic force constant of 100kjmol-1A-1 is applied to
all nonhydroggen protein atoms.
In my pr.mdp file which parameter I should add?
Thank you very much!
_
> Dear users:
> I have a position restrain .mdp file need to set,I use 300K
> in which an isotropic force constant of 100kjmol-1A-1 is applied to
> all nonhydroggen protein atoms.
>
> In my pr.mdp file which parameter I should add?
> Thank you very much!
If you use pdb2gmx, it will ge
Dear users,
How do I restart a gromacs simulation?
Ciao,
Luciano
Dr. Luciano Triguero College of Art and Science Department of Physics and
Chemistry Cox Science Building 1301 Memorial Drive, Room 146 P.O Box 249118
Coral Gables, FL 33124-0431 Cellular: 305-904-2419 Office: 305-284-3938
_
tpbconv
Catch ya,
Dr. Dallas Warren
Lecturer
Department of Pharmaceutical Biology and Pharmacology
Victorian College of Pharmacy, Monash University
381 Royal Parade, Parkville VIC 3010
[EMAIL PROTECTED]
+61 3 9903 9524
-
When the only tool you own is a hammer, ever
Dear users:
My protein is large,so I use genbox -shell 1.2 to add water,
Then I genion -conc 0.15 -neutral, At last,In .top file I find 7703 water,
but there are 183 Na+,170 cl-,I want to know whether ions is too more.
Is this normal?
Could somebody tell me?
> Dear users:
> My protein is large,so I use genbox -shell 1.2 to add water,
> Then I genion -conc 0.15 -neutral, At last,In .top file I find 7703 water,
> but there are 183 Na+,170 cl-,I want to know whether ions is too more.
> Is this normal?
> Could somebody tell me?
How about find
Hi,
The concentration of pure water is 55.6M. So, 1 ion with a single charge
per 556 molecules of water equals 0.1M.
Ran.
Mark Abraham wrote:
>> Dear users:
>> My protein is large,so I use genbox -shell 1.2 to add water,
>> Then I genion -conc 0.15 -neutral, At last,In .top file I find 7703
Hi Andrea,
I have a program to look at the coordination number and other things
for cations and oxygen ligands. Maybe that could help... If you want,
I can send it to you.
Best,
Tsjerk
On 3/16/07, [EMAIL PROTECTED] <[EMAIL PROTECTED]> wrote:
Hi all,
I am struggling with the rdf. I have 7 stru
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