ord, after all. Even
> now I can't find the right word. I slipped up twice.
>
> I apologize for my mistake -I basically took from you a few minutes
> because of my lack of clarity :)
>
> Cheers,
> Michel
>
>
>
> On Thu, Feb 14, 2008 at 11:47 PM, Tsjerk
Hi,
grompp allows you to write the (cpp) processed topology (-pp). Since
many parameters are controlled using cpp #define statements, cpp has
to be called to fill the values. pdb2gmx can't do that.
Cheers,
Tsjerk
On Feb 15, 2008 6:46 PM, Alan Dodd <[EMAIL PROTECTED]> wrote:
> If you convert the
Hi,
You may have written only a subset of atoms to the new trajectory
files using trjconv. Keep track of what you're doing and what is in
which file. Besides, most analysis tools also accept .pdb/.gro files
for reference.
Cheers,
Tsjerk
On Feb 15, 2008 6:31 PM, Justin A. Lemkul <[EMAIL PROTECTE
Hi Pascal,
Please specify the (Gromos) force field used further. There seems to
be something with the 53a5/6 series in terms of alpha helix / beta
sheet preference. I'm not sure whether this has been fixed already. I
don't recall having heard of such an issue with the 43a2/45a3 series.
But these h
Hi Justin (and Geraldine),
I think that cross-referring people asking about building topologies
to the exotic species wiki page by default is a bit too much. It's
Parameterization they need to read (and chapter 5 of the manual).
Exotic species are those weird atoms you sometimes encounter in
ligan
Hi Chandu
> Because I am using NPT ensemble will it automatically adjust to that
> density? (because box size will increase under high temperature and
> constant pressure therefore density will be decreased)
Yes.
But don't expect to get right on with the density (or
viscosity/diffusion/...).
Hi David,
If you use a structure file (.gro/.pdb) which corresponds to the
starting structure and has the protein and ligand in the right place,
you can do it with trjconv -pbc nojump.
Cheers,
Tsjerk
On Sun, Feb 24, 2008 at 4:47 AM, David Osguthorpe
<[EMAIL PROTECTED]> wrote:
> On Sun, Feb 24,
Monika,
Daniel has already given the answer. The third column gives the
standard deviation, whereas the second gives the average SAS. You
could've found this answer also by browsing the mailing list archive,
as this is one of those questions being posted every once in a
while...
Cheers,
Tsjerk
Hi Jo,
First of all, you should note the difference between essential
dynamics analysis and sampling. Also note there's nothing essential
about it. But the first is done using g_covar/g_anaeig and the latter,
which concerns enhanced sampling along specific modes, is done using
make_edi/mdrun. So i
Hi Alan,
Unfortunately there have been server problems (severe hacking) in
Groningen some while ago, and the NDLP server was terminated. But,
we're right about to reestablish an improved server here in Utrecht.
This server will be much faster, seconds rather than hours - the
optimal packing for th
Hi Lal,
Well, if you set the number of steps to 0, it should get you rid of any errors.
But for the rest, the LINCS errors don't have to do with the length of
the simulation but with what's in there.You can try and decrease the
time step as is suggested by the program. But the LINCS error is
likel
Hi Lacerda,
You should be cautious in the interpretation of your results. Your
active site will only be minimized in potential energy in the context
of your frozen surface and your restraint internal degrees of freedom.
You should be very confident that your surface is about correct and
your inter
as not able to download the modified versions of the code at
> http://md.chem.rug.nl/~tsjerk/GMX/ where this method is implemented.
> I was wondering if anyone has implemented it in some newer version of
> gromacs as Tsjerk Wassenaar did for 3.2.1.
>
> I am reading the relevant pape
No, but you should try to distinguish an O (letter-O) from a 0 (numeric zero).
Tsjerk
On Wed, Mar 19, 2008 at 3:54 PM, Gadzikano Munyuki
<[EMAIL PROTECTED]> wrote:
> I want to do dynamics on a cyclic polypeptide. The peptide contains a residue
> that is not standard Ornithine. I have added [ORN]
ot quite sure
> about the reference to the pair of pdb files. Would a way to do this be to
> say project the first and second eigenvector and then use Dyndom to compare
> the starting structure with the first eigenvector extreme pdb and then do
> the same for the second? Would this sh
Dear Lal,
It would help if you mentioned the commadns you used and whatever else
you tried.
Maybe it's a good time to read http://catb.org/~esr/faqs/smart-questions.html
Tsjerk
On Sat, Mar 29, 2008 at 8:56 AM, s lal badshah <[EMAIL PROTECTED]> wrote:
> Dear Experts,
> Hi, I have done equilibrati
Hi Jo,
> > Also if I am comparing the SASA for the enzyme in
> > three different simulations were only the ligand (for which all radii are
> > defined) differs, would this have a huge effect on the results?
Your question is semantically garbled. You comparing anything should
not influence the
here.
Sorry for the previous babbling... The reference to the wiki still goes though
Cheers,
Tsjerk
On Wed, Apr 9, 2008 at 9:24 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Jayant,
>
> PO3 seems to me the anion of metaphosphoric acid, not much to do with
> phosph
Hi Jayant,
PO3 seems to me the anion of metaphosphoric acid, not much to do with
phosphoric acid. The latter could be sort of extracted from phosphoric
acid containing residues, although that doesn't give guarantees for
good behaviour. Also, I wouldn't count on the PO4 parameters thus
extracted to
Hi Peggy,
I suspect that in your .mdp file you have a line
xtc-grps = Protein
This means that the xtc file will only contain those atoms which
gromacs reckognizes as amino acids, based on the list in the file
aminoacids.dat. Your .tpr file which is used to base the index on,
contains all atoms,
, I had: xtc_grps = protein Ca Cl
>
> Will this difference cause the problem? How should I solve it? Thanks a lot!
>
> Peggy
>
>
>
> On Thu, Apr 10, 2008 at 12:22 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]>
> wrote:
>
> > Hi Peggy,
> >
> > I suspect that
matching reference structure?
>
> Thanks a lot!
>
> Peggy
>
>
>
> On Thu, Apr 10, 2008 at 11:52 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]>
> wrote:
> > Hi Peggy,
> >
> > The key thing is that there's a mismatch between your .tpr file and
> &
I beg your pardon.
What do you think we are? The equivalent of a fast-food take-away? Or
a service for doing your homework for you?
Do take a good read of http://catb.org/~esr/faqs/smart-questions.html
Tsjerk
On Mon, Apr 21, 2008 at 1:28 PM, shahrbanoo karbalaee
<[EMAIL PROTECTED]> wrote:
> hi a
Hi Arnab,
If you know the time at which you want to start the analysis, you can
use the -b option (with whatever analysis tool). E.g. starting rmsf
calculation at 1 ns:
g_rmsf -s topol.tpr -f traj.xtc -o rmsf.xvg -b 1000
Cheers,
Tsjerk
On 5/5/08, Arnab Senapati <[EMAIL PROTECTED]> wrote:
> Hi,
Hi David/Makoto,
I wouldn't call it a stupid error, keeping nine numbers for the
definition of a box. Of course in simulation the lower triangular part
of the box matrix is zero. But if you reorient the system and want to
preserve PBC (like after fitting), the box will be rotated and the
full matr
Hi JS RED,
This usually indicates that you have a mismatch between your reference
structure and your trajectory, which is logical as you extracted a
specific set of coordinates from the trajectory, but used an original
(complete) gro file.
Hope it helps,
Tsjerk
On Thu, May 8, 2008 at 9:18 AM, m
Hi,
Maybe good courtesy to sign with a bit more than some initials. It's
so much nicer to have a bit of the impression to know whom you're
talking to.
As for the question, if you would select 'Protein' to extract a part
of your system to a trajectory, this part would likely be the first N
atoms f
Hi Xavier,
Have you checked the genome and made sure your potato did not suffer
from any infection? This will have a significant effect on the melting
temperature. Maybe it helps if you link an image of the potato at the
end of the simulation.
Tsjerk
On Sun, May 11, 2008 at 12:23 AM, Xavier Peri
Hmmm,
Now imagine your simulation system as a say 1000 nm3 portion of a
liter. For that liter you work out the number of ions and you properly
translate that into an amount of ions you expect in the 1000 nm3. But
then your protein (floating along in the same liter in some small
concentration) cros
Hi Servaas,
> trjconv -f fit.trr -o cluster.trr -n lig_prot.ndx -pbc cluster -s top140.tpr
I think there's quite a bit of reason to start calling you names here :)
Assumedly, fit.trr means that it results from fitting the trajectory
to a reference?
So what does this do with your PBC?
> I also tr
Xi Zhao,
If you know these steps are normal, how come you don't know how to go
about? A projection on the plane spanned by two eigenvectors is the
projection of your structure onto one of these eigenvectors plotted
against the projection of your structure on the other. Each structure,
and therefor
Hoi Servaas,
Was that the trajectory for a given temperature, or for a given
system? It should be for the latter, as otherwise, there will be weird
shifts introduced. A trajectory for a given system, over the different
conditions should be (from the PBC point of view) continuous and it
should be p
Hi Tuhin,
It depends on what you do. In both cases you will have to run grompp
with an index file with a group specified, containing both the Protein
and the calcium ion. You can take an existing index file (created
simply with "echo q | make_ndx -f mystructure.gro") and add the number
of the calc
Hi Nadir,
First of all, nm / ps^2 for acceleration was not a choice, but a
consequence of other choices. Second, it's meaningless to pull this
out of context. There's no reason whatsoever not to have a huge
accelaration, if it is only for short times. It's the speed that
counts, not the accelerati
Hi Carmen,
You really have to be careful to match the .rtp to the .pdb building
block. pdb2gmx indicates that there's an atom in the .pdb file, which
is not found in the [ CHIT ] entry in the .rtp file. If you want
better help, you'll have to ask a better question: you should provide
more details
Hi sh-karbalaee,
Well, running an MD simulation has nothing to do with genion per se.
But it's better not to have a net chare in your system. Therefore
you'd best add an ion (at the least) to your system with unit charge.
Whether you do that using genion or do it by hand, is entirely up to
you. Ch
Hi Carmen,
Well, adding a residue to aminoacids.dat only makes sense for amino
acids (although I admit to fiddle it sometimes, in which case it is
usually best to make a local copy). But one thing with amino acids is
that backbone -N(H)-Ca-C(O)- thing, which is referred to in the
termini database.
Anandita,
Just to add my response on the pile (and do take the previous advice)
what you show here displays a problem of yours with respect to
molecular dynamics simulations. That naming should be consistent,
sure, if you know what you're doing you can sort of ignore warnings
like 'atom names don'
Hi,
For a tutorial and a workflow you can also check out:
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/
http://www.nmr.chem.uu.nl/~tsjerk/course/md-tutorial/01-Preparation-Workflow.jpg
A bit in progress still, and any comments welcome ;)
Cheers,
Tsjerk
On Sat, Jun 21, 2008 at 9:40 AM,
Hi,
Of course I can't add anything to the comments regarding the solvent and ions ;)
The #include "ions.itp" is commonly added through pdb2gmx in the >3.1
versions, so it shouldn't be necessary to add that (and it isn't for
the tutorial (v3.3.3). Anyway, it's good to keep in mind though that
the i
Hi Minnale,
You could've checked the archives. Searching on "trr" and "deleted"
would have yielded (among others):
http://www.gromacs.org/pipermail/gmx-users/2008-May/034217.html
Tsjerk
On Tue, Jun 24, 2008 at 5:40 AM, minnale <[EMAIL PROTECTED]> wrote:
>
> Hi gmx users,
> I have deleted
Hi Sunita,
You should check the manual on this (and some statistics texts on PCA).
g_covar calculates the average structure and takes the deviations
around this average for further calculations. In that respect, you
should be save. But the fact that you pose this question indicates
that you may be
Hi Ram,
Check the option -merge of pdb2gmx.
Cheers,
Tsjerk
On Thu, Jun 26, 2008 at 6:11 AM, rams rams <[EMAIL PROTECTED]> wrote:
> Dear Gromacs users,
>
> Is there any way to handle the disulphide bond formed between two
> independent fragments of a protein ? Precisely it is an inter disulphide
Minnale,
A file is (generally) data on a disk, of which the operating system
knows where it is. Knowing where the file is depends on the inode of
the file. Deleting a file is usually removing the inode, not the data.
But once the inode is removed, the data can no longer be recognized as
a certain
Hi,
The only thing I can think of is that you've run pdb2gmx already and
added the termini (adding H1 H2 and H3 for the terminus, which causes
the complaints). Now, you're running pdb2gmx for the second time
(right?) to merge the chains. Next to -ignh you can also try to simply
remove these N-term
Browse the archives, check the wiki.
http://wiki.gromacs.org/index.php/Periodic_Boundary_Conditions
Tsjerk
On Fri, Jun 27, 2008 at 8:06 AM, Bhanu <[EMAIL PROTECTED]> wrote:
> Hi all,
> am new to Gromacs. I tried a 10 ps simulation with a protein and after the
> run, the protein came out of the bo
Hi,
That doesn't necessarily "fix" the "problem". Which position of the
protein is taken as a reference depends on the position of the first
atom. Gromacs wants to have the first atom of a molecule in the
rectangular unit cell at the origin. Even if you set comm removal for
the group, the initial
Hi William,
I'm not very sure you can simulate crystallization of salt with
classical MD. In any case, the force field is not parameterized to
reproduce crystallization or melting c.q. the melted state of NaCl.
It's therefore unlikely that it will produce meaningful results. The
best approach :) w
Hi,
Well, I think it should also be incorporated into (Gromacs) MD
tutorial material. It's on my to do list. I don't think there's much
use in adding a message in the mdrun output (might as well always add
it, not even checking for jumps). It's basic PBC, which, with a bit of
thinking, can be unde
Hi Minnale,
You could try another version as was suggested... Never hurts to try.
The magic number error occurs if the file is screwed. trjconv will
correctly process the trajectory up to the point where the magic
number error occurs, so you can restart from the last good entry in
the file. Out of
Hi Sudheer,
I would say you just try to add a nanosecond to a run which still has
ten to go (10+1=11). That also tells me you're not trying to extend a
run already performed (properly), as it has a starting step of 0
(starting time 0.000). Then on another note, it seems that you didn't
copy-paste
As I stated in the first sentence, I doubt the usefulness of classical
MD for simulating crystallization of NaCl. Whatever I state after that
applies to the case of trying it with classical MD nonetheless. Please
read closely before trying to outwit however you find on this list.
Second, as is cle
Hi Grange,
It recognizes the possibility of having a bond between these atoms.
That's where the distance matrix comes in. But if a bond were made,
you'd have a statement right after the distance matrix saying
something like "linking atom ... and atom ...". It doesn't happen, and
the reason is the
Hi Cesar,
Not with tpbconv. You can do it with grompp, adding the .trr end .edr
file you have as input and making sure that you don't generate new
velocities and set unconstrained_start to yes.
Cheers,
Tsjerk
On Sun, Jun 29, 2008 at 10:18 PM, Cesar Avila <[EMAIL PROTECTED]> wrote:
> I found the
Minnale,
Please do read the following:
http://wiki.gromacs.org/index.php/Errors
This one's in there.
Tsjerk
On Mon, Jun 30, 2008 at 11:26 AM, minnale <[EMAIL PROTECTED]> wrote:
>
> Hi all,
> 1) I have embedded protein into popcbilayer
> 2) Energy minimisation
> 3) Later added ions by usin
Hi,
use trjconv
Well, that's just to start the mail with it in stead of ending. g_rms
(g_gyrate, g_rmsf, g_covar) are rather dumb programs, taking a
structure, fitting it to a reference orientation and doing some stuff
on it. They don't check for jumps over the PBC. PBC and fitting don't
go too w
Hi Rui,
In the previous version of the gromos force field, the hydrogens on
these groups would be collapsed to the carbons. In the newer force
fields (53*) they are treated explicitly, but I think NADH has not yet
been reparameterized.
Cheers,
Tsjerk
On Mon, Jun 30, 2008 at 9:14 PM, Joaquim Rui
Hi Travis,
It looks like grompp doesn't parse your .mdp file properly. You should
get an mdout.mdp which contains the parameters as they ended up in
your .tpr file. Check these against your .mdp file. Alternatively you
can 'gmxdump' your .tpr file to check the parameters. Was the .mdp
file origina
Lin,
This is manual stuff...:
http://www.gromacs.org/documentation/reference/online/g_angle.html
So the first lines answer your question:
g_angle computes the angle distribution for a number of angles or
dihedrals. This way you can check whether your simulation is correct.
With option -ov you ca
Hi Anirban,
Might it be of any use, here's a structure/topology of glucose based
on the GROMOS96 53a6 force field.
Hope it helps,
Tsjerk
On Thu, Jul 3, 2008 at 12:44 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
> Use whichever one you think will best represent your molecule. I think some
>
Darn.., forgot the attachment.
>
> On Thu, Jul 3, 2008 at 1:16 PM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
>> Hi Anirban,
>>
>> Might it be of any use, here's a structure/topology of glucose based
>> on the GROMOS96 53a6 force field.
>>
>>
Hi,
Read a bit more carefully though. A cubic box is based on the
circumscribed sphere of the solute, dilated with the desired distance
between the solute and the wall (and it has nothing to do with
calculation of the solvation surface, which to me sounds to be related
to solvent accessible surfac
Alok,
If you want to see the symmetry as in the crystal, try and simulate the crystal.
It may well be that in the absence of crystal packing forces a certain
degree of asymmetry is favourable.
Tsjerk
On Sat, Jul 5, 2008 at 12:54 AM, Alok Sharma <[EMAIL PROTECTED]> wrote:
> Dear All,
>
> I have t
Hi,
Besides, there are parameters around for DPPC for the newer GROMOS96
force fields. PRODRG is unlikely to yield better results. Better check
literature (Marrink's group, Tieleman's group). That is, unless
there's a specific reason to use PRODRG, e.g. comparing results with
standard parameteriza
rom
> PRODRG. Now, I used DPPC pdb file from Tieleman's web site and I produced
> Gromos96 ff from PRODRG again. At the begining, it seems bond lengths
> between phosphate and oxygens are very long but during the minimization they
> come to expected values.
>
>
>
>
>
Prasun,
You're really messing things up here! You should get to terms with the
gromacs manual. Read up on the different file types and how things are
connected. To start with, gromacs doesn't care whether it's given a
.pdb file or a .gro file for coordinates. So everywhere where it says
you can re
Hi Harshith,
The GROMOS96 force fields are united atom force fields, so it makes
sense to use the model without explicit non-polar hydrogens. However,
as you can see in the topology, the aromatic hydrogens are treated
explicitly.This is to allow for some charge separation, emulating the
negativity
Prasun,
Starting with the end (the last question is easiest).
> Apart from this i am interested in learning how to create .itp
> file,can you please suggest any method.
Reading! A very good method of learning things. It's how I learned to
do these things.
> So can you please send me the detail
Hi,
Well, about .itp files. itp simply means "Include ToPology", i.e. a
file to be #include-d in a topology file. In most cases here on the
list it is used to designate a file which contains a [ moleculetype ]
description. The [ moleculetype ] is explained in detail in the manual
chapter 5. In sho
Hi Ramon,
Zinc should be considered as one of those "exotic species"
(http://wiki.gromacs.org/index.php/Exotic_Species). It's almost
impossible to give a set of parameters which will work for all zinc
binding sites. Actually, it's best to parameterize based on the
environment. Now, if you have QM/
Hi Hui Sun,
Did you verify the integrity of the trajectory with gmxcheck? If not,
you should and if you find that the trajectory is not good, show us
what's wrong. If the trajectory is not garbled, but is interpreted
wrongly by VMD, try the VMD user list.
Tsjerk
2008/7/19 hui sun <[EMAIL PROTECT
Willons,
For such issues we have the gmx-users list. Please post questions
there (subscribe if you haven't already done so). Actually, you can
find the answer in the archives of this list. Flattery will bring you
nowhere (well, at least it will keep me gentle in my reply ;))
Advantages of the user
Hi,
I had noticed it too, but (in the rush) haven't looked into it
anymore. To me it also appeared to be a bug. Please provide some input
which reproduces it and file a bugzilla.
Tsjerk
On Wed, Jul 30, 2008 at 8:42 AM, David van der Spoel
<[EMAIL PROTECTED]> wrote:
> G.H. Zuo wrote:
>>
>> Hello
Hi,
Otherwise, divide every element ij by sqrt(ii)*sqrt(jj).
Cheers,
Tsjerk
On Wed, Jul 30, 2008 at 4:44 PM, Ran Friedman <[EMAIL PROTECTED]> wrote:
> I made a modified version of g_covar that has this capability. I'll put it
> in the user contributions later today.
>
> Ran.
>
> Dhananjay wrote
Hi Prasun,
As a side-note to the replies of Justin and Florian, why not take the
following approach?:
1. run pdb2gmx on the monomer, giving structure and topology for one unit
(2. energy minimize in vacuum)
3. use editconf to make a transformed copy of the monomer
-- now, you know for sure that b
Hi,
A displacement is not a fluctuation. Displacement is also relational,
so you'll have to specify with respect to what. Likely you'd interpret
displacement with respect to the mean structure, which by definition
is at zero on a given principl axis. But in that case, the
displacement is more comm
-- Forwarded message --
From: sunita gupta <[EMAIL PROTECTED]>
Date: Fri, Aug 1, 2008 at 1:12 PM
Subject: plotting the displacement of each C-alpha along first
eigenvector having largest eigenvalue
To: [EMAIL PROTECTED]
Hello
I have done 15 ns MD to study the effect of point muta
Hi Inon,
Please be as complete as you can when posting questions. You've
omitted the (probably) most important piece of information: what
version are you using? (You might also want to include platform, OS,
compiler, etc.). Note that just a few days ago it was already reported
on this list that g_
why RMSD?
On Tue, Aug 5, 2008 at 9:19 AM, David van der Spoel
<[EMAIL PROTECTED]> wrote:
> wang kelvin wrote:
>>
>> hi:
>> i am doing simulation of a system consists of 512 DMSO moleculers and
>> 917 water moleculers.
>> the whole system is running under 290K and 1bar ,and constraints = none;
>
Hi,
On Fri, Aug 8, 2008 at 3:12 PM, Vitaly Chaban <[EMAIL PROTECTED]> wrote:
> No problem, Prasun. :) Just open conf.gro and see the last string
> there. Divide the least number by 2 and type it in the grompp.mdp as
> your new cutoff.
>
This is a good way of turning gromacs into the well-known e
Hi,
Well, sed's a good friend to have in these cases :)
e.g. converting lysine residue names:
sed -e 's/LYSH/LYP /' -e 's/LYS/LYN/' gromacs.pdb > amber.pdb
or converting the C7 of thymine to C5M:
sed -e 's/\(^.\{13\}C\)7 THY/\15M THY/' gromacs.pdb > amber.pdb
Note that this can be easily exten
Hi :)
Maybe these little scripts are useful...
The first, titratable.sh (use: titratable.sh file.pdb), generates a
list of residues for which the protonation state can be set, including
the termini. The second, gmxquery.sh (use: titratable.sh file.pdb |
gmxquery.sh) gives a series of 0 1 2, accor
Well,
sed -ne '{/^\(ATOM\|HETATM\)/{s/^\(.\{21\}\)\(.\)\(.*\)$/\2\1\2\3/;p}}'
file.pdb | sort | cut -b 2- > sorted.pdb
sort of seems to do the trick. But it will place the chainless things first.
Hope it helps,
Tsjerk
On Tue, Aug 12, 2008 at 3:13 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
Hi Rebeca,
In the GMX data directory ($GMXDATA) there's a file aminoacids.dat
listing what should be recognized as amino acids. Either edit the file
and add HIE (also incrementing the counter at the top line) or make a
local copy of the file in the directory where you need it and edit
that.
Cheer
ASP A 131 -1.040 -15.548 4.997 1.00 51.90
> C
> ATOM 80 OE1 GLN A 33 7.692 11.421 46.868 1.00 70.33
> O
>
> Kindly suggest any way to correct the .pdb file so that it can be converted
> to .gro file
>
> With Thanx,
> Vivek
>
> 2008/8/12 Tsje
ach separate
molecule and combine these later on. If you don't understand what I'm
talking about, don't do it; pick another protein.
Cheers,
Tsjerk
On Wed, Aug 13, 2008 at 7:37 AM, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
> Hi Vivek,
>
> Sorry, I should've been
Hi Sridhar,
pdb2gmx adds all hydrogens _according to the force field definition_
(and a database file describing how to add which hydrogen where).
If you want to have all hydrogens "satisfying the valencies", you need
to choose a force field that includes them, i.e. an all-atom force
field. Maybe
Hi beibei,
When asking such questions, it is vital to provide information about
your OS. Linux, Windows, Mac? Do you use (ba)sh, (t)csh or some other
shell. Wouldn't hurt to understand a bit more about computers and
terminology if your research depends on them.
Linux:
(ba)sh: export GMX_NO_SOLV_O
Hi Minnale,
We do appreciate that english is not your native language (it isn't
mine either), but please try to write correct, complete sentences.
That will make it easier to read your posts, understand what you did
and where you went wrong and how we can, maybe, provide you a
solution.
Justins r
Hi Vitaly,
Do you have a rather fixed ratio between the two? ion:solvent = 1:10
e.g. Then you could make an arrangement of a single ion with
surrounding solvent and replicate that with genconf. You could even do
a short simulation setting rvdw to less than half the size of your
small box :p for a
Hi Parthiban,
Do you have a particular reason for using the MPI version of trjconv?
Do you have the same error with the standard version?
Cheers,
Tsjerk
On Mon, Aug 18, 2008 at 6:12 AM, M.Parthiban <[EMAIL PROTECTED]> wrote:
> Hi
>
> I am encountering an error in file conversion from .trr file
Hi Parthiban,
Well, it was the best possible shot in the dark. Then please enlighten
us with more information: What is your command line? What platform do
you use? Which compiler? When did it work? What system?
Cheers,
Tsjerk
On Tue, Aug 19, 2008 at 5:55 AM, M.Parthiban <[EMAIL PROTECTED]> wrot
Please also note that *do_dssp* is part of the gromacs suite, and is
basically a wrapper around the third-party program *dssp* from CMBI,
calling it for every frame and processing the output. do_dssp relies
on the environment variable DSSP for locating dssp.
Tsjerk
On Mon, Aug 18, 2008 at 9:07 PM
Ah, sure, now we know!
Well, actually I almost confirmed my suspicion, just searching for
libc.so.6 in the archives. But first, you might want to read
http://www.catb.org/~esr/faqs/smart-questions.html
Then, you can continue with
http://www.gromacs.org/pipermail/gmx-users/2007-November/030605.html
Hi Lin,
If you include bromide, you won't have excess charge... So, no need
for adding more counterions.
Cheers,
Tsjerk
On Thu, Aug 21, 2008 at 8:20 AM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote:
> Hi
> It is the water-molecule system.
> For a molecule, like R-N(CH3)3-Br, I could make a pdb fil
Vitaly,
This is not a grompp warning, but a warning from one of the analysis
tools. grompp will never take masses 'out of the blue', but will
always use the force field description (atom type definitions) or the
mass specified in the .top/.itp file. It will bail out if no mass is
properly defined
Lin,
A .gro file does not have information regarding masses. Therefore, any
operation involving masses (mass-weighted fitting) will not be
performed optimally.
Cheers,
Tsjerk
On Thu, Aug 21, 2008 at 9:19 PM, Chih-Ying Lin <[EMAIL PROTECTED]> wrote:
> Hi
> As you described...
> This is not a
Hi,
In this specific case it could be worth replacing writing .xtc files
(using xtc-grps, nstctxout, etc) with writing .trr files in the code.
That wouldn't be a lot of work (if you know a bit of C-code ;)).
Cheers,
Tsjerk
On Sun, Aug 24, 2008 at 5:26 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wr
Hi Alka,
This list is not for posing riddles and puzzles, although they may be
interesting ;)
You should give all relevant information, or think carefully yourself.
Actually, it may be helpful to reformulate your riddle and let you
think about it... :p
If your cubic box has dimensions of 6 nm an
Hi Parthiban and Sundar,
Did you check the .trr file with gmxcheck?
By the way, is this still that same (faulty) trjconv of these
sysadmins of yours who compiled it with gcc 4.x?
Cheers,
Tsjerk
On Wed, Aug 27, 2008 at 8:36 AM, <[EMAIL PROTECTED]> wrote:
> hi all
>
> i can able to get .trr fi
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