;
>
> Best regards,
>
>
> Mijiddorj
>
> --
>
> Message: 5
> Date: Sat, 22 Oct 2016 10:11:50 +0200
> From: Tsjerk Wassenaar
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] D-amino acids' force fields
&g
Hi Mijidorj,
These amino acids are chemically and topologically equivalent to their L
counterparts. For united atom force fields you only need to invert the
improper dihedral at the C-alpha. For atomistic force fields you don't need
to change anything, except the CMAP stuff in Charmm for the backb
Hi Sophia,
I can't help out with mdrun -membed, but I did write a tool (insane) to
avoid just the hassle you seem to face. It builds a coarse grained system,
but that can be converted to atomistic. Depending on what exactly you need
to do, it may be trivial or less so. In either case, if you care,
_gmx-users digest..."
> >
> >
> > Today's Topics:
> >
> >1. Umbrella sampling tutorial (gozde ergin)
> >2. principal component analysis chain break (??)
> >3. Re: principal component analysis chain break (Tsjerk Wassenaar)
> >
&g
Ni hao Jie,
The extreme projections are typically pretty meaningless. But if you want
them or the more meaningful PCA output, do make sure you remove jumps over
PBC from your input trajectory and have the molecules whole/clustered.
Cheers,
Tsjerk
On Oct 7, 2016 11:21 AM, "胡杰" wrote:
> Dear Gr
Hi Surya,
The first part ss a warning, not an error. It also says (implicitly) that
if the molecules are not broken across PBC then there's nothing to worry
about whatsoever. So just assert that your molecules are not split over
PBC. Have a look at the trajectory. If there are frames with one part
Hi Alvaro,
gmx genconf
Hope it helps,
Tsjerk
On Sep 29, 2016 4:59 PM, "ÁLVARO RODRIGO RUIZ FERNÁNDEZ" <
arr...@ug.uchile.cl> wrote:
> Dear gromacs users:
>
> How I can multiply a box full of molecules from 1x1 to 2x2 ?, I know I can
> use Avogadro but in this case it does not work, I think fo
Hi Sanket,
gmx trjconv allows writing frames based on a frame index file or using a
xvg file and threshold. Check the help of trjconv on it.
Hope it helps,
Tsjerk
On Thu, Sep 29, 2016 at 9:05 AM, Sanket Ghawali
wrote:
> Dear, gmx-users,
>
> I performed a cluster analysis using gmx cluster. I
t motions of only ligand, along a particular
> direction (say rotation along a dihedral in ligand) from this trajectory?
>
> Best Regards
> Ashutosh
>
> On Mon, Sep 26, 2016 at 3:52 PM, Tsjerk Wassenaar
> wrote:
>
> > Hi Ashutosh,
> >
> > To simplify this,
Hi Ashutosh,
To simplify this, let's do PCA of two balls on opposite ends of a stick I'm
rotating. The mean position of both ends is right at the center of
rotation, and the relative positions I can describe with X and Y
coordinates only. Now, the essence of PCA is the question 'which single
direc
Hi George,
Oh, quadrants over PBC, so it just completely ruptured. It means the area
per lipid is really off in your starting structure. Where did you get it
from?
Cheers,
Tsjerk
On Sep 8, 2016 3:54 PM, "George Pantelopulos"
wrote:
> Dear Tsjerk and Erik,
>
> Thank you for the responses!
>
>
Hi George,
How did you build the starting structure?
The quadrants are due to distribution over cores/nodes. You can try EM on a
single core for a few steps, but it seems that the system is too stretched
anyway, so I think that won't really solve your problem.
Cheers,
Tsjerk
On Sep 7, 2016 11:
Hi Jernej,
This is simpler in two dimensions:
Consider a hexagonal unit cell.
Draw it, together with the surrounding copies (7 hexagons total).
Now connect the central hexagon with the right horizontal neighbor, and
with the 'northeast' neighbour.
Connect these two neighbors with their other commo
Hi Elka,
Methyl asparagine is not known by DSSP and is not availble in Martini.
You're probably best off replacing it by asparagine:
sed '/^ATOM/s/MEN/ASN/' 1HG0.pdb > out.pdb
Cheers,
Tsjerk
On Fri, Aug 26, 2016 at 11:26 AM, Elka Firmanda wrote:
> Hi, I just got "X" amino acids on DSSP, what
Hi Arnost,
When you fit with rotation the coordinates and the box are not on par
anymore. Anything you do after that tries using PBC will fail. I guess that
Plumed is trying to use the box to get the COM-COM distance. The only
(practical) solution: don't fit.
Cheers,
Tsjerk
On Aug 17, 2016 00:2
Hi Yasser,
Probably you're using semi-isotropic pressure coupling, which you should
only do if you have a membrane like structure aligned with the XY plane (or
a somewhat stiffish wire like structure aligned along z).
Cheers,
Tsjerk
On Wed, Aug 10, 2016 at 3:52 PM, Yasser Almeida Hernández <
ya
Hi Sanket,
That's not really a Gromacs question, is it? And it's pretty simple math,
once you decide what you mean with 30%. You may want to check
https://en.wikipedia.org/wiki/Concentration
Cheers,
Tsjerk
On Fri, Jul 29, 2016 at 7:44 AM, Sanket Ghawali
wrote:
> Dear, gmx-users,
>
> Hello eve
Hi Gayathri,
For the XTC file you used only a selection of atoms to write out. The TRR
file always contains everything. With the conversion from TRR to XTC make
sure to write the same selection as is in the other XTC files.
Hope it helps,
Tsjerk
On Thu, Jul 28, 2016 at 7:36 AM, GAYATHRI S wrot
etween 'single' molecule at specific 'z' of the box
> indicating the phases .
>
> So I think my given way is easier, but not sure if the reruns goes like the
> original simulations?
>
>
> Best regards
>
>
> On Mon, Jul 18, 2016 at 12:57 PM, Tsjerk Wa
Hi Faezeh,
You could use gmx select to make groups for the two phases and then perform
a rerun with these new groups as energy_grps. That would give you the
within and between group energies.
Hope it helps,
Tsjerk
On Jul 18, 2016 12:49 PM, "Faezeh Pousaneh" wrote:
Hi,
I have a Phase-separati
e
> either the topology is bad or the starting structure has clashes that
> cannot be adequately addressed using EM or because of improper
> parametrization.
>
>
> On Sat, Jul 16, 2016 at 3:43 PM, Tsjerk Wassenaar
> wrote:
>
> > Hi Swagata,
> >
> > That's
Hi Swagata,
That's not a problem. You should be fine running a simulation, given the
potential energy of the system. Check the archives for more elaborate
comments on this matter. And please check the archives/google before
posting questions. We like breaking our heads over new, tough issues, and
Hi Deep,
What force field? What system? How many cores? Did you try running on one?
What error? Did pdb2gmx or grompp give any warnings?
Cheers,
Tsjerk
On Wed, Jul 13, 2016 at 5:44 AM, Deep Bhattacharya
wrote:
> Hello,
> My system is blowing up for the protein carbohydrate solvent complex. I
Hi Venkat,
First, note that there are no such things as hollow ('vacuum-filled' :p)
proteins in nature. Simulating a capsid without contents is probably
non-sensical.
Besides that, you could try insane (http://cgmartini.nl/index.php/insane).
By default it excludes the inside of a protein for place
Hi Gregory,
There is no default position restraint during EM. Of course, one wouldn't
expect them to move much and one would expect the local energy minimum to
be rather close to the initial position, if you used an equilibrated water
box to set up the system.
Cheers,
Tsjerk
On Jul 8, 2016 08:38
Hi Suniba,
Don't look at the cosine content. It doesn't convey anything useful. If you
want to know more, I've posted more lengthy remarks about it before.
Cheers,
Tsjerk
On Jun 27, 2016 1:11 PM, "Sun Iba" wrote:
> Hello Users and experts
>
> My system details:
> Force field: GROMOS 43a1
>
> G
Hi Albert,
Rotate the system 90 degrees and use PBC in xy only.
Cheers,
Tsjerk
On Jun 26, 2016 9:04 AM, "Albert" wrote:
> Hello:
>
> I've got a membrane protein system and I would like the water and ions
> only wrap in XZ direction. Currently, they can also wrap at Z direction. I
> am just won
Hi Qasim,
If you fit a trajectory, with trjconv -fit rot+trans, then each frame is
fit onto the reference.
Hope it helps,
Tsjerk
On Tue, Jun 21, 2016 at 11:12 AM, Qasim Pars wrote:
> Dear users,
>
> From GROMACS online manual:
> gmx confrms computes the root mean square deviation (RMSD) of tw
Hi David,
And why the number of frames?
Cheers,
Tsjerk
On Tue, Jun 21, 2016 at 9:52 AM, David van der Spoel
wrote:
> On 21/06/16 09:40, Qasim Pars wrote:
>
>> Dear David,
>>
>> Could you please more explain each term of the formula you said?
>>
>> Formula=The number of atoms (N * 3)^2 times n
Hi Phil,
Did you write all atoms to the trajectory or only a group? Does the
reference structure match the trajectory? The Jacobi error usually occurs
when there is a mismatch, and the route via a PDB file is consistent with
that.
Cheers,
Tsjerk
On Sat, Jun 18, 2016 at 3:25 AM, Phil Dude wrote
Hi Sanket,
You probably want the clustering routine of trjconv. And then calculate the
principal axes of the micelle. The instantaneous value does not mean much,
but a an average non-zero eccentricity would suggest with a greater extent
than without peptide would suggest an effect. Note that you d
Hi Qasim,
Not only should you neutralize the system, but you should add additional
ions too. The behaviour of charged side chains which can find a partner ion
from solution is different from those that can't. You won't see any
problems, but the results will be affected. Not coming across any probl
upposed to converge. Maybe you want
> to verify something else?
>
>
> From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se <
> gromacs.org_gmx-users-boun...@maillist.sys.kth.se> on behalf of Tsjerk
> Wassenaar
> Sent: Monday,
Hi Amit,
What membrane and what time scale are you talking about? Complex membranes
may take microseconds to equilibrate.
Cheers,
Tsjerk
On Jun 13, 2016 06:13, wrote:
> Hello everyone,
> I built a lipid membrane in Charmm-GUI and tried to equilibrate it in
> GROMACS 5.1.2. But the total energy
Hi Agnivo,
In addition to the remarks of Andre, if you can show that another US run on
the same system gives pretty much the same result, then you can present
that as proof of the robustness, and it is futile to do three more,
especially if you have convergence and sufficient overlap. You can
high
Hi Qasim,
The RMSD is not good for assessing convergence, especially if it goes above
0.5 nm.
Cheers,
Tsjerk
On Wed, Jun 8, 2016 at 8:48 PM, Qasim Pars wrote:
> Dear users,
>
> I have simulated a protein with simulation time of 200 ns and saving the
> coordinates at every 40 ps. Conformation
Hey :)
> That usually gives a fitted ensemble that more closely retains the
> original RMSD values between all pairs of structures.
>
This should read: ... a fitted ensemble of which the sum of the traces of
all pairwise inner product matrices is closer to minimal.
The pairwise RMSDs (and thei
Hi James,
That's silly! Ambiguous means that the same structure can have multiple
solutions in a fit. The fit to a single reference structure (with more than
three atoms) is never ambiguous. Can never, by definition!
Now if you have two reference structures at hand, and they have (quite)
differen
Hi Teresa,
You probably want to try clustering, and then check the percentage of
bound/unbound structures in the clusters you get. Just the RMSD won't tell
you much.
Cheers,
Tsjerk
On Wed, Jun 8, 2016 at 11:30 AM, ingram wrote:
> Dear GROMACS community,
>
> I am trying to identify the number
Hi James,
'Spurious alignment' is the dependence of the resulting ensemble on the
reference structure. Unfortunately, that's not solved by a progressive fit.
Rather, in a progressive fit, the same configuration can have multiple
orientations, based on the previous structures, which is also problem
Hi Teresa,
No, the peptide should not be broken. Did you remove jumps over PBC?
The peptide will probably be severely distorted by filtering, though.
Cheers,
Tsjerk
On Wed, Jun 8, 2016 at 8:49 AM, ingram wrote:
> Dear GROMACS community
>
> I am trying to complete a PCA analysis of my peptide
Hey :)
There's a suggested workflow on the Gromacs site:
http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions
Cheers,
Tsjerk
On Jun 7, 2016 11:50 PM, wrote:
> I solved the problem by using an em.tpr with pbc nojump for my dimers. pbc
> whole takes the monomers as whol
I couldn't find anything about that on google.
>
> Cheers,
>
> On 7 June 2016 at 15:15, Tsjerk Wassenaar wrote:
>
> > Hi Qasim,
> >
> > What makes you think that they should start at 0,0 ?
> > The overall mean of any set of projections lies at the origi
Hi Nidhin,
It looks like you have a version of insane that still builds oleyl with
five beads. It should be four as 'CDCC' like you did for building the
topology. So you also need to remove the C5 beads and shift the D to
position two. Then you should be set to make/simulate your bilayers.
Cheers
t; structure (Md. Imrul Reza Shishir)
> > 2. cannot output all the structures of one cluster (Zhenyu Meng)
> > 3. Re: Non-bonded energy (ABANTIKA PAL)
> > 4. Re: gmx gangle selections help (Teemu Murtola)
> > 5. Re: DPPC-DOTAP Mixed Lipid Bilayer (Tsjerk Was
Hi Apramita,
No restrictions. You're in charge. To get a correct density, you'll need to
equilibrate with pressure coupling.
Cheers,
Tsjerk
On Tue, Jun 7, 2016 at 1:08 PM, Apramita Chand
wrote:
> Hey,
> Thanks a lot Tsjerk for your advice regarding box size. You've mentioned
> that we coul
Hi Qasim,
What makes you think that they should start at 0,0 ?
The overall mean of any set of projections lies at the origin.
PCA is a pretty powerful and advanced technique, that requires quite a bit
of thinking in the preparation, the execution and the interpretation.
Please do read plenty of tu
Hi Apramita,
First of all, your box diameter should be the length of the peptide plus 2,
with a minimum of 2.8. Otherwise, the peptide will be able to interact
directly with its periodic image.
The solvent is typically added by overlaying a box of pre-equilibrated
solvent and deleting all molecul
Hi Nidhin,
Insane allows you to build lipids from the command line. Alternatively,
it's pretty easy to add DOTAP to insane, using the templates inside. If you
feel you need a hand with that, let me know.
Cheers,
Tsjerk
On Jun 7, 2016 12:21 AM, "Nidhin Thomas"
wrote:
> Hi GROMACS Users,
>
> I w
Hi Williams,
It looks like you didn't set the Gromacs include directory. What
command/procedure did you use to compile?
Cheers,
Tsjerk
On Jun 3, 2016 21:25, "Williams Miranda"
wrote:
> Dear GROMACS users
> I use gromacs 4.6.5, then, I downloaded trj_cavity v1.1 for installation.
> But I am get
Hi Qasim,
Do you assume MWC or KNF like allostery, and conformational based, dynamics
based or mixed?
Cheers,
Tsjerk
On Fri, Jun 3, 2016 at 2:54 AM, Qasim Pars wrote:
> Dear gmx users,
>
> The protein I have simulated over 200 ns with GROMACS is dimer and shows
> positive allostery. Based on
Hi Qasim,
The plot you refer to is the result of NMA on C-alpha only. So g_covar
-xpma using only C-alpha atoms should come close. You might also want to
try the g_correlation tool mentioned earlier on the list, but again with a
selection of only C-alpha atoms.
Cheers,
Tsjerk
On Fri, Jun 3, 201
Hi Irem,
pdb2gmx checks the hydrogen bonding network and decides which form of His
fits best.
Cheers,
Tsjerk
On Jun 2, 2016 17:20, "Irem Altan" wrote:
> Hi,
>
> When I process a .pdb structure using pdb2gmx, how does Gromacs add
> hydrogens to the histidine residues? I see that in the processe
Hi Riccardo,
The boolean options are specified as -m or -nom, without further arguments.
For non-mass-weigthed you want -nom.
Hope it helps,
Tsjerk
On May 27, 2016 15:49, "Ravasio Riccardo" wrote:
> Dear gmx users,
>
>
> After performing Normal Mode Analysis, I would like to print a non
> mass
Hi Sourav,
For Martini there's the conversion script martinize, which has an option
-nt to suppress putting charges on termini.
This is not really a Gromacs question, and it's better to post Martini
related questions on the forum at http://cgmartini.nl
Cheers,
Tsjerk
On May 24, 2016 23:35, "Jus
Hey :)
If you just have the .tpr and you don't want to use Gromacs' tools, you can
use python:
python -c 'import struct; print
"".join(struct.unpack(100*"c",open("YOUR-TPR-HERE").read(100)))'
(Python 2, mind you).
Cheers,
Tsjerk
On Mon, May 23, 2016 at 11:33 AM, Mark Abraham
wrote:
> Hi,
>
Hi Sapna,
How should we know how many clusters you should have?
A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's
what you want/need or whether that's meaningful/helpful for your goals is
something you should consider. We don't know what you're trying or doing.
Cheers,
Oh, you don't want to dump one frame! You want the frames beyond 25 ns. So
don't use -dump at all. You'll only get one frame though, using a spacing
of 1 ns.
Cheers,
Tsjerk
On May 21, 2016 13:53, "Tsjerk Wassenaar" wrote:
> Hi Antara,
>
> You indicate you w
Hi Antara,
You indicate you want the frame at 27ns (-dump 27000), but that's not in
the trajectory. The suggestion is to ask for a frame that is in, like -dump
25290
Cheers,
Tsjerk
On May 21, 2016 13:09, "Antara mazumdar" wrote:
Dear gromacs users,
I was trying to dump structures from MD.t
Hi Nikita,
It's not like there's a range to take a minimum from. It's this with this
force field and that with another. Any deviation will alter the behaviour
of the force field, and you'll have to show that the result is valid,
either by running tests, or by referring to a paper that has results
Hi Antara,
You can also simply calculate the ratio of buried surface area to total
surface area, which you can both get with gmx sasa
Cheers,
Tsjerk
On Thu, May 19, 2016 at 3:10 PM, Sarath Chandra <
sarathchandrada...@gmail.com> wrote:
> You can use g_contacts tool which will give you list of
Hi Nikita,
That's actually a good question, and I think it hasn't been phrased like
this before. I rephrase it slightly again, so it says "which parameters
should be considered part of a force field?"
The first thing that springs to mind is not really a parameter, but a vital
part of the force fi
Hi Sanket,
The problem is that a charge group moved too far between two domain
decomposition steps.
Seriously, we can't say more than that, unless you tell us more about the
system and how you got to the point where you are.
Cheers,
Tsjerk
On May 18, 2016 8:44 AM, "Sanket Ghawali" wrote:
> *D
Hi Sanket,
You can use 'gmx traj' to write the COM over time.
Cheers,
Tsjerk
On Wed, May 18, 2016 at 7:09 AM, Sanket Ghawali
wrote:
> Thank you Justin. I am sorry, I didn't make my query specific.
>
> g_dist calculates distance between COMS of 2 groups with reference to time.
> I want to moni
Hi Sanket,
Can you check the structure in the tpr file (editconf -f .tpr -o
.gro/.pdb)? If that is good, then -pbc nojump should work. For the second
pass, you shouldn't need -pbc mol then.
Cheers,
Tsjerk
On May 16, 2016 9:06 AM, "Sanket Ghawali" wrote:
> Dear, gmx-users,
>
> Hello everyone,
>
o variables with free energy? like
> RMSD and Rg?
>
>
> Sent from my iPhone
>
> > On 15-May-2016, at 10:51 am, Tsjerk Wassenaar wrote:
> >
> > Hi Suniba,
> >
> > No, with gmx anaeig you can select -2d, which does a 2D projection onto
> the
> &
Hi Suniba,
No, with gmx anaeig you can select -2d, which does a 2D projection onto the
selected eigenvectors. Alternatively, you can combine any two projections
onto eigenvectors, which you get using the option -proj. The quickest way
to do that is something like:
paste <(grep -v '^[@#]' proj1.x
Hi Upasana,
What is your goal, your research objective? 'opening it for docking
purpose' is way too vague for us to help you, other then suggesting that
you are probably not choosing an optimal approach.
Cheers,
Tsjerk
On May 14, 2016 07:04, "Upasana Ray" wrote:
> Dear user,
>
> I have gener
Hi Antara,
What commands did you use? At least make sure you add -rdd 1.6 to the
command line of mdrun, because the default value is too small for coarse
grain simulations.
Cheers,
Tsjerk
On Fri, May 13, 2016 at 8:12 PM, Antara mazumdar
wrote:
> Dear users,
>
> I am trying to run a coarse gra
Hey :)
Salt water has a higher density than pure water anyway.
Cheers,
Tsjerk
On Apr 26, 2016 5:19 PM, "Christopher Schlicksup"
wrote:
> Thanks Justin. I was expecting closer to 1000kg/m^3. My reading about the
> tip3p water model found approximately this value at 300K, and it is also
> the ap
Hi Sana,
There's no such thing as a standard volume. The key decision you have to
take is what distance there should be between periodic images, for which
the consensus view is that you need at least 2.0 nm. I typically use 2.25,
corresponding roughly to 9 layers of water, so the protein can stret
Hi Suniba,
For the first part, look up 'periodic boundary conditions' (my oh my, there
should be a keyboard shortcut for that term). For the second part, it seems
you have loaded two files, and you should see two objects in the right side
panel of Pymol. You can turn visualization off by clicking
Hey,
In addition, for Q3, sure you can have a program build you acetonitrile
from the interactions. But what about cholesterol? Morphine? A protein? For
just a bit more complicated stuff, let alone the really complicated stuff,
you need to have coordinates to start with.
Cheers,
Tsjerk
On Apr 14
right!
Cheers,
Tsjerk
On Apr 14, 2016 05:32, "Brett" wrote:
> Dear All,
>
> If the issue in my production MD was caused by
> "Periodic_Boundary_Conditions", I can continue my production MD until it
> completed, and it will not affect my final results suppose I have it
> corrected by trjconv, ri
Hi Gregory,
Yes, these steps are deterministic. Think of where the randomization should
come from. Sure, there is 'random' placement of ions in genion, but it has
a default seed, resulting in deterministic random numbers :)
Hope it helps,
Tsjerk
On Apr 9, 2016 00:33, "Gregory Poon" wrote:
> He
s. This could be easily done by g_density with an .ndx file. I need
> to
> > have a plot of density-time for each of the components of the system.
> >
> > Please help...
> >
> >
> >
> >
> > Best regards
> >
> >
> > On Wed, Apr 6, 2016 at
>
> Best regards
>
>
> On Wed, Apr 6, 2016 at 4:58 PM, Tsjerk Wassenaar
> wrote:
>
> > Hi Faezeh,
> >
> > Using -b/-e flags you can get the density profile over a window of time
> (or
> > a single frame). Afterwards you can combine the results to h
Hi Faezeh,
Using -b/-e flags you can get the density profile over a window of time (or
a single frame). Afterwards you can combine the results to have a density
profile over time.
Hope it helps,
Tsjerk
On Wed, Apr 6, 2016 at 4:29 PM, Faezeh Pousaneh wrote:
> Hi,
>
> Is it possible to obtain p
Hi Mijiddorj,
For a biologically stable alpha-helix, you should not use any restraints.
If you want to stabilize a helix that is known to fold/unfold, then try
something not too stiff. Usually like 100 kJ/mol/nm^2 should already do.
But again, don't try to 'fix' a force field in this way.
Cheers,
Hi Saeed,
Us a larger box, like edge length 2.5 or 3. The non-matching names are not
much of a problem, and you can add -maxwarn 1 to the grompp call.
Cheers,
Tsjerk
On Apr 2, 2016 8:29 AM, "Saeed Nasiri" wrote:
> thank you TsjerkI modified the topology file and did all the thing from the
> be
Hi Saeed,
Just before [ molecules ] insert the lines:
[ system ]
A box of water
Cheers,
Tsjerk
On Apr 2, 2016 8:06 AM, "Saeed Nasiri" wrote:
> Dear users
>
> I have constructed a box of only water molecules, but I don't know how to
> constructed the topology file. I wrote this file but it did
No, what Mark means is that if you equilibrated temperature AND pressure
(NpT) there's no point in an NVT step, in which the pressure may go off
again, even though it's unlikely to matter much, because the volume is
already within proper range.
However, there's the 'posre' part still, which sugges
:
> You could try to fit first (-fit rot+trans) and fix pbc (-pbc nojump)
> later.
>
> Cheers,
>
> Fra
>
> On 31 March 2016 at 05:45, Tsjerk Wassenaar wrote:
>
> > Hi Irem,
> >
> > Check the structure in nvt_water_frozen.tpr:
> >
> > gmx editco
Hi biohpc,
For this you need to combine output from gmx hbond, gmx sasa, and gmx
saltbr.
Cheers,
Tsjerk
On Mar 31, 2016 12:58, "bio hpc" wrote:
> My problem is not excel or whatever graphical program. I just need the
> data, in an automatic way. Then I can use either matplotlib or similar to
>
Hi Irem,
Check the structure in nvt_water_frozen.tpr:
gmx editconf -f nvt_water_frozen.tpr -o ref.pdb
Cheers,
Tsjerk
On Mar 31, 2016 00:04, "Irem Altan" wrote:
> Hi,
>
> I am simulating a protein in its unit cell. I use the original .pdb file
> as an input, so the initial molecule is not frag
Hey :)
-ignh does ignore the hydrogens in the input file. It builds those
hydrogens that are specified in the force field. For histidines, the
protonation state is determined from the possible hydrogen-bonded network,
but it is possible to assign specific states interactively, using the
option -hi
Hi Brett,
There is no GROMACS force field. Now the original GROMOS force fields 53a5
and 53a6 are known to be more unstable in the helix department than they
should, so better not use those. There are newer versions of 53a6 and
there's 54a7, which are fine. I'm actually not entirely sure what vers
Hi Irem,
The correction vectors is internal bookkeeping stuff, making sure to keep
track of what is where in a computationally efficient manner.
To get rid of this, I think the best option is to rotate your unit cell, to
have the largest vector (your third) along the x-axis. The second largest
sh
> > > the correct choise influence on sampling here`? E.g in full atomistic
> > > sims generally langevens dynamics produces better results in
> > > comparison to berendsen thermostat which produce very unphysical
> > > behaviour for the macromolecular systems.
> &g
sjerk, does it make sense to try to have grompp observe the particle
> density and guide the default of -rdd accordingly?
>
> Mark
>
> On Wed, Mar 23, 2016 at 9:19 AM Tsjerk Wassenaar
> wrote:
>
> > Hi James,
> >
> > Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or
Hi James,
Try setting -rdd 1.4 in mdrun. Sometimes 1.5 or 1.6 is necessary
(especially if you use a larger time step, like 30 fs).
Cheers,
Tsjerk
On Mar 23, 2016 09:08, "James Starlight" wrote:
> Hello,
>
>
> I am trying to perform 2 MARTINI simulations of several membrane
> receptors within m
Hi Shyno,
Is there a difference in mass-weighting? Can you try on C- alphas only?
Cheers,
Tsjerk
On Mar 16, 2016 15:55, "Shyno Mathew" wrote:
> Dear all,
>
>
> I wrote a tcl script to do cluster analysis, using gromos method. My
> results are slightly different from the g_cluster results. I se
Hey :)
You can define any box 'shape', expressed in terms of the corresponding
lattice vectors, compliant with the rules stated in chapter 3 of the
manual. You can set a hexagonal prism cell using editconf, using the -box
and -angles options. In your case, the long edge should be along x, and has
Hi Stephane,
The difference is too large for rounding errors. I was not suggesting
different selections, but rather mass-weighting versus non-mass-weighting.
Cheers,
Tsjerk
On Mar 17, 2016 23:15, "Téletchéa Stéphane" <
stephane.teletc...@univ-nantes.fr> wrote:
> Le 16/03/2016 16:54, Shyno Mathe
Hi James,
Yes, that is possible too. If you need a hand, contact me off-list.
Best,
Tsjerk
On Mar 17, 2016 16:32, "James Starlight" wrote:
> btwh dont understand clearly the whole methodology
>
> for instance If I have coarse'grained system obtained from the
> martinize tool consisted of the 1
le format has to be a pdb format. However, if
> I have a trajectory ( in xtc format) and each frame's 'bfactor' values are
> getting updated, then do I need to convert entire xtc files into pdb files
> for visualization?
> Jagannath
>
>
> On Tue, Mar 8, 2016 at
and rerun the simulations:
>
> continuation = no
> gen_vel = yes
> gen-seed = -1
>
> Right?
>
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himac
t; changes I have to make and in which .mdp file?
>
> Best Regards,
>
> *Neha*
>
> Research Scholar,
> Centre for Computational Biology and Bioinformatics,
> School of Life Sciences,
> Central University of Himachal Pradesh,
>
>
>
>
>
> On Wed, Mar 9,
Hi Neha,
You can perform a simulation first, and then extract configurations, which
you simulate with new starting velocities. Alternatively, you can generate
a number of different starting structures using elastic-network modeling,
like with the ElNemo server. Mind to first energy minimize the re
Hi Jagannath,
Convert the file to PDB format and write the values to the b-factor field.
Most visualization programs can color by b-value.
Cheers,
Tsjerk
On Mar 8, 2016 06:50, "Jagannath Mondal" wrote:
> Dear gromacs-users
>
> I am sorry to write you a visualization-related query. I hope you
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