A couple of months ago someone mentioned a recent publication that went
through a procedure for the detection of an interface / surface between
phases for data from MD. Remember reading the publication and thinking
was pretty neat and need to come back and try it. Well, for the life of
me can't f
Shouldn't you just do it anonymously?
git clone git://git.gromacs.org/gromacs.git
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3
the file try2-water-ions.pdb.
>
> Thanks and regards,
>
> lina
>
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
> Sent: Tuesday, June 15,
What is the contents of the CRYST1 line in the file try2-water-ions.pdb?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
--
not
> reach this steps. The problem I had just the steps I did the energy
> minimization after ions (NA+ and CL-) added.
>
> Thanks and regards,
>
> lina
>
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
>
Please copy and paste in the commands you are using, and the output.
I suspect you have made your box bigger, but it still contains the same
number of molecules and you still have pressure coupling on. So when you
start the simulation, not surprising that the box compresses again and
goes under 2n
I would make a new residue in the .rtp file.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
> I think Dallas might have been thinking of a different file; function
> types are
> not required in individual .rtp entries, but you do have to have a
> proper
> [bondedtypes] directive at the top of your .rtp file. A few other
> comments:
Yes, sorry. In my case I define the type in the variou
You have no function types defined in your bonds, angles and dihedrals.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
---
If you are referring to something that will generate a coordinate file
(.pdb or .gro) of polymer molecules randomly distributed, then there is
not currently a script with GROMACS that will do that job. If you have
a single molecule, there are a couple of tools that can randomly spread
those molecu
> I seem to say this several times per week: in my experience (and in
the
> experience of many others who have posted here) the charges and charge
> groups output by PRODRG are often unsatisfactory, requiring manual
Might be an idea then to put the comments on the PRODRG page on the
GROMACS websit
--
> Program g_sdf, VERSION 4.0.5
> Source code file: gmx_sdf.c, line: 177
>
> Fatal error:
> For single particle SDF, all reference groupsmust have the same size.
>
> ---
>
> Nilesh
>
>
> On
pr -mode 1 -o sdf.plt -r
>
> Nilesh
>
> On Mon, May 17, 2010 6:37 pm, Dallas B. Warren wrote:
> >> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt
> -r
> >
> > Is that the exact command line you used? If so, doubt it would
> actually
&g
> g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s -mode 1 3.tpr -o sdf.plt -r
Is that the exact command line you used? If so, doubt it would actually
work, since it should be:
g_sdf -f 3.trr -n glu-emi-cl-128-no.ndx -s 3.tpr -mode 1 -o sdf.plt -r
Catch ya,
Dr. Dallas Warren
Drug Delivery, Dispositi
You can call the following whatever you want to:
[ moleculetype ]
; Namenrexcl
Protein 3
This would probably be more appropriate:
[ moleculetype ]
; Namenrexcl
Hexane 3
And this section, doesn't really matter what it says here either, this
par
For starters there is no residue name in your .gro file, you simply have a
number. First column should be …
1HEX C1
1HEX C2
.
.
.
1HEX H14
2HEX C1
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parad
It is most likely due to having the order of your molecules in the
topology file (.top) different to those that are in coordinate file
(.gro).
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Pa
See section 5.7.1 of the manual , it shows you exactly how you define
angles, bond, dihedrals etc for any type of molecule in the topology
files for GROMACS. If after the theory, see section 4.2
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceut
What are the atoms that are causing the problems actually doing, where are they
located etc?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+
Isn't that already present in the energy file, .edr, from the run?
Simply use g_energy to extract it.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.mona
Probably already seen it, or beyond it now, but a good primer is
http://www1.lsbu.ac.uk/water/models.html
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.mo
g_energy
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hamm
If you have aggregation and a small box size, then the rdf will not be
able to asymptote to one.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.ed
You are going to have to provide a lot more details than that if you
want some help.
What is "wrong results"? What is your input (copy and paste some
commands in)? What is the output (copy and paste)? What makes you
think the results are "wrong"? In what situations are they "right"? ...
and
> Thanks David. These are the parameters I added. Do you think they seem
> reasonable?
You might as well run a simulation yourself, it will be quickly apparent
if something is very wrong.
Best way to determine these things is try it and see for yourself.
Catch ya,
Dr. Dallas Warren
Drug Deliver
Why is it that what you have run with xy rigid and z couple not correct?
Fluctuating box volume is exactly what you would expect to get, and do get,
with pressure coupling.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monas
Actual text input / output would be a good idea here. What is the actual
output when you try to run it the second time?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dall
Can you run that same procedure without doing anything to your protein?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
A single methane molecule in water, it is not surprising at all that
there is some noise in the rdf produced. If you want it smoother than
that, you will simply having to run it for longer. The rdf is an
average, insufficient data points mean it will be noisy, you cannot get
around that fact.
Ca
So, what EXACTLY are you doing?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the o
Have a read of
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations in
particular the section down the bottom that is appropriate for the
version of GROMACS you are using.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Scien
Might be a good idea to provide the input and output that generated the
error.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 91
Wouldn't it be simpler to just exclude the intramolecular -OHs when you
actually generate the RDF?
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
From: gmx
FYI, there is a listing in bugzilla
http://bugzilla.gromacs.org/show_bug.cgi?id=356
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
<>--
gmx-users mailing listgmx-users@gromacs
t has undergone a polar transformation
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Dallas B. Warren
Sent: Wed 12/16/2009 8:25 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] g_sdf and visualizing using gOpenMol
Rename it to .plt might be a good
Rename it to .plt might be a good start, since that is the file extension it is
meant to have (as noted in the help information for g_sdf).
Also, there is an issue with the reference structure built was the script, it
is not correct. Has been noted by a couple of people. Been meaning to check
Another option is to create a new trajectory file to use in your analysis,
using trjconv
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
From: gmx-users-bou
transformation
-Original Message-
From: gmx-users-boun...@gromacs.org on behalf of Mark Abraham
Sent: Fri 12/11/2009 11:33 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] fftw vs cmkl
Dallas B. Warren wrote:
> Thanks Mark.
>
> My stats on this, GROMACS 4.0.7 comp
Thanks Mark.
My stats on this, GROMACS 4.0.7 compiled with gcc, run on two quad-core Xeon
processors with 16GB of RAM, 100,000 atoms, PME, 200,000 steps
fftw 3.2.1 - 20,027 seconds
Intel cmkl - 19,792 seconds
So about 1.2% faster.
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Scienc
Just wondering if anyone has done a comparison of GROMACS complied using fftw
versus cmkl?
SC tech suggested that cmkl might be a bit faster, but can't find any mention
of someone making a comparison between them anywhere, searching users list and
web for "cmkl" (is there may be another term us
Command lines that you use? Contents of the index files? Contents of the
output files?
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
From: gmx-users-bou
First three groups are the reference group, from which the SDF is generated, it
sets the coordinate system. That means you need to have at least three "atoms"
in the "molecule" you are generating the SDF from.
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A
trjconv
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a hamme
...@gromacs.org] On Behalf Of Manik Mayur
Sent: Saturday, 21 November 2009 1:06 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Hydrated radius of ions
2009/11/20 Dallas B. Warren
g_rdf ?
Thanks, but while using g_rdf, when I have lots of ions, do I have to
make an ndx file
http://www.gromacs.org/Documentation/How-tos/Extending_Simulations
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
When you try to minimise, it will typically tell you the worst offending
atoms in your system. Which you can then check visually using VMD etc
and try and work out why it is an issue. Then you can adjust how the
system was set up to fix the issue.
Also, if you just look at the system visually
g_rdf ?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is a ha
Coordinate files like pdb and gro aren't used by GROMACS to provide any
bonding information. That is what the topology files are for. So their
"presence" in your pdb isn't an issue.
Actually, what is probably happening is that PyMol is guessing the bonds
presence, based on the distance betwee
How are you visualizing the system? Using VMD? In that case, bonds are
determined by how far apart the atoms are, it guesses what the bonding
is, since a .gro file (or a pdb) doesn't have any bonding information in
it. So what you are seeing is simply the fact you have scaled the box,
increasing
Omar's response answered that question on why they are different. In
the first one you are grouping all three into one group, second is just
one of the hydrogen types. The fact that the rdf you get is different
indicates that all three hydrogens are not identical. Have you compared
the rdf for e
Plot the fluctuations of the pressure with time for the simulation. Far
better way I think to get an idea of what is going on with a property
than just looking at values in a log file. Especially when you are
starting out.
With pressure coupling, it is not unusual to have a fluctuation of a
h
> No. My system is a single protein with charged ligand associated with it. But
> why should box size shrink ? In solvated system it does not shrink. What
> effect vacuum could possibly have on it ?
Sounds very much like you have pressure coupling on. Check your .mdp file.
Catch ya,
Dallas Wa
You don't really need to do anything. Atom number simply starts again.
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
From: gmx-users-boun...@gromacs.org o
If the time frame between snapshots is not too short, you could have
that as the length of each MD run, then simple extend the run to keep on
going. Could be a bit inefficient. (This is how you should run MD
anyway, to ensure don't lose a lot of information if the computer system
you are running
> Dear All,
>
> when I want to use grompp program
> grompp -f minim.mdp -c solboxbrady.gro -p bradymod.top -o
> minimbrady.tpr
>
> I got the following error message
>
> Fatal error:
> [ file "spc.itp", line 41 ]:
> Atom index (1) in settles out of bounds (1-0)
>
> So I tried to m
If there isn't one in the forcefield already, then it is something that you
have to parameterise yourself.
Catch ya,
Dr Dallas Warren
Pharmacy and Pharmaceutical Sciences
Monash University
A polar bear is a Cartesian bear that has undergone a polar transformation
-Original Message-
F
Best if you don't mess with the ones that are installed. Set up your own
forcefield files in a local directory and edit those, GROMACS scripts will then
look in the local directory first, before going to the installed one.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharm
How is it that the date and time is wrong? It is simply telling you
that the simulation will be completed on Sep 16, using the time on the
computer that the program is running on.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash Unive
You might want to consider the parameters I developed for propylene
glycol http://dx.doi.org/10.1021/mp8001667 ... might provide some
guidance for you in terms of the parameterisation of ethylene glycol.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceu
Have you managed to minimise a single molecule?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When t
Suggest you have a look and search the VMD emailing lists. These sorts
of visualisation discussions come up from time to time with people
sharing their experiences.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal
> Maximum force = 9.4016180e+02 on atom 31
As has already been suggested, have you looked at the atoms listed as having
the maximum force to see why?
>Addtionally, the structure of the solute is incorrect (all atoms are bonded to
>each other).
How are you visualising it? If using VMD, th
> You indicate that I need to read the primary literature for the force
> fields. Could you please tell me where this literature can be found? I
> have searched using Google for the forcefields available for use in
> GROMACS (G43b1, G43a1, G43a2, G45a3, G53a5, G53a6, gmx), but have not
> found any
> And, by the way, I have resolved the segmentation fault problem. It
was
> being caused by the freezing of the graphene lattice. When I removed
> the
> freezing, I saw the graphene structure curl upward and am thinking
that
> by freezing the atoms in place it was creating great forces between
the
>Maximum force = 4.9815813e+24 on atom 169274
You should have a look at that atom, that is a large force.
___
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://ww
The error tells you what the problem is:
Fatal error: reading tpx file (em.tpr) version 40 with version 20
program
You are trying to read an em.tpr file that was generated using version
40 (as noted by the header it is GROMACS 3.3.1) using a version 20
program (as noted by the header it is
Because pdb2gmx has to know what residue(s) are contained in the .pdb
file, and the third column identifies the residue and as the program has
told you, it is called "1". And it does not have a "1" residue on the
.rtp file associated with that forcefield.
Catch ya,
Dr. Dallas Warren
Department o
Two ways:
1 - turn them off with the visualisation software you are using, only
display the protein and lipid
2 - use editconf and the appropriate index groups
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash Un
What exactly do you mean by "unusual cross bonds"?
I suspect what you are seeing is simply a visualisation artifact, with a
molecule being displayed across a PBC in the viewer you are using.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceut
The error message explicitly tells you what is wrong:
"Expected 2 elements for wall_atomtype, found 0"
And looking in your .mdp file ...
;WALLS
; Number of walls, type, atom types, densities and box-z scale factor
for Ewald
nwall= 2
wall_type= 9-3
wall_r_linpo
Just as Mark and Justin have said, this is up to you to define this
question.
The reason I said that, is you were asking "how do I know if my molecule
is docked to the protein?". The first step to answering that question
is defining what you mean by being docked. Once you have a definition,
then
Exact same question was answered just last month .
http://www.gromacs.org/pipermail/gmx-users/2009-April/040974.html
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 301
http://wiki.gromacs.org/index.php/Errors#Residue_.27XXX.27_not_found_in_
residue_topology_database
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.
I would recommend you have a read through the appendix in the GROMACS
manual titled "Manual Pages". This has all the scripts provided with
GROMACS and the manual page for them, which describes what each one
does. Reading through that will go a long way to letting you know what
you can and can't d
http://www.gromacs.org/pipermail/gmx-users/2006-December/024953.html
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
First step, define what you mean by being "DOCKed".
Second step, determine if those conditions are meet by your protein and
ligand.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Pa
Run input file = .tpr
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only
Sorry, but I only performed a couple of runs using the test-set, so
don't have a lot of experience, but when I did and got some fails all
the information was there to help point out what the issue was.
Doesn't the files in the subdirectories for each of the tests provide
details of why that partic
Check consistency with other entries around it, easy way to check to see that
you have the right format.
What did you edit the file with?
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, P
epeating units. Do you
> mean I can write the rtp entry for one repeating unit and give it a
> residue name. After that I need to insert this into the force field
> rtp file, right? How can I do that? It seems I can not change the rtp
> file. Thanks.
>
> On Tue, Apr 28, 2009
If it is a repeating unit, then you can build a .rtp entry then use it as you
would for a protein.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.mo
The issue is you don't have enough statistics to get a meaningful
result. Three ways you can get more, more particles, more time, or
multiply runs.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Roya
Best idea is to ask the vmd people, they have their own emailing list.
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a polar
transformation
On 28/04/2009, at 12:29 PM, "He, Yang" wrote:
HI Mark,
I am indeed using the coarse-graining atoms .What do you mean b
z-axis is the length of the cylinder, parallel to the straight sides.
x-y is in the plane of the circle cross section of the cylinder.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkvi
Both of those errors are telling you want you need to do. In your
topol_A.itp file, there are no parameters for a particular proper
dihedral. So, define one. Same with the next message. And it even
tells you which line the issue is on in the .itp file, so very easy to
track down which bonds are
Well, as the error says, popc isn't defined in the index file. Seems
grompp is looking for a popc entry in the index file, and can't find it.
So, I would hazard to say, you need to define it.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmace
That is entirely up to you.
The forth paragraph in the help explains how the three atoms in the
index are used to generate the coordinate system.
Best idea with anything like this, have a play, see what comes out, see
if it is what you want, then try again. Play with it like that will
also help
What exactly your issue with using g_sdf?
You need to supple a trajectory, index, and topology. Index contains
the three reference atoms for the molecule, plus the atom you are
calculating the sdf to. Selection of the correct grid size and binwidth
is required to get something that looks as you
Another to keep an eye out for, is make sure that you edited the correct
.rtp file you tell pdb2gmx to use when running it.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 301
May be have bit of a read of
http://wiki.gromacs.org/index.php/Category:Force_Fields and the manual,
so you can get a grip on what forcefields actually are and how you use
them.
I get the impression you are trying to do things here without actually
understanding or even thinking about what you are
Or g_sdf
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
-
When the only tool you own is
g_angle will do that fine, and with the options you used it should have done
so. Possible issue that may make that fail is you failed to generate the
correct angle index file for the dihedral(s) of interest.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Ph
Might I suggest that you refer to this webpage
http://wiki.gromacs.org/index.php/Errors
It would have answered both of your error questions you have posted.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
> > Is there a way to reduce the fluctuations of the properties
> calculated
> > with g_energy?
> Fluctuations scale as 1/sqrt(N) where N is the number of
> molecules. So
> the answer is yes.
Depending on what you actually want to do, some smoothing of the data
may be what you are after. One
Kim,
>Recently I have been focusing on cross-linking phenomenon of polymers.
>As far as I understood, cross-linking include bond breaks in one
polymer chain and bond occurrences among broken chains.
>I guess OPLS-aa is not suitable for this purpose, and my question is
this.
>Is my guess correct?
No, the molecule has not gone out the side of the box and not entered
the other side. If you check the solvent on the opposite side of the
box, you will notice that there is a big hole that exactly matches up
with the DNA fragment that is sticking out. Use the pbc options in VMD
to display neighb
The _d denotes that the command is the double precision version.
Command does exactly the same things, just at double precision which
may or may not make any difference to the result.
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a polar
transformation
On 18
Berk that would be handy. Option in that, could you may be have not to
change the name at all and use the names specified on the command line?
Catch ya,
Dallas Warren
A polar bear is a Cartesian bear that has undergone a polar
transformation
On 17/02/2009, at 6:01 PM, "Berk Hess" wrote:
Chris,
> One option is to avoid checkpoint files all together. I personally use
> a grompp/mdrun cycle of ~2h segments that was historically done in
> order to utilize the -sort -shuffle options to gromacs 3. I found it
> simpler to keep on doing the exact same thing in gromacs 4, even
> t
Justin,
>> When using checkpoint files to continue a run, mdrun overrides the output
>> file names specified by putting ".part" before the file extension.
>>
>> I don't want it to do that, since I have already told it how I want the
>> output files to be named.
>>
>> Is it possible to stop
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