Hi all,
I have simulated a system of LJ molecules. I have used reduced
units. My box size was 8.58. No of molecule was 442. I have run a
NVT simulation. The runtime was 200 ps. After simulation the
reduced energy/per molecule i got was 4.29 which is acurate
(checked from Hailee). But the pre
You will find useful information here:
http://wiki.gromacs.org/index.php/Carbon_Nanotube
as well as by searching the list archives. CNT questions arise fairly often.
-Justin
Quoting Mayank Verma <[EMAIL PROTECTED]>:
>
> Hi,
>
> I'm facing problems with creating topology of CNT.
>
> I have a
Hi,
I'm facing problems with creating topology of CNT.
I have a x,y,z coordinates for the SWCNT which (10, 10), has 800 atoms, 1160
bonds, bondlength: 1.4520 A and tube length: 50.
I need the toplogical information about this CNT. how to go about it, using
GROMACS or anyother software?
T
Dear Bob,
> Yes...sorry...I'm doing a 7.5 ns for each lambda value (lambda = 0,
> 0.25, 0.5, 0.75, 1.0). Every single simulation takes place from the
> exact some starting configuration. No restraints are being used. The
> calculation I'm planning on doing (once everything is worked out) is a
> re
I'm continuing to look at this stuff. Just a quick sanity checkat
lambda=0.5 I should be getting equal and opposite values for
for the forward and reverse reactions. Is that correct?
Thanks,
Bob
On Thu, May 8, 2008 at 11:56 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote:
>
> Perhaps a naive
Perhaps a naive question, but which version of Gromacs are you using? Such
issues are well-known in 3.3.1, but have been fixed in the most recent release
(3.3.3).
-Justin
Quoting Robert Johnson <[EMAIL PROTECTED]>:
> Hi Maik,
> That's exactly what I'm attempting to do...morph G to A etc. All I
Hi Maik,
That's exactly what I'm attempting to do...morph G to A etc. All I'm
doing here is turning off the charges of G and then turning them on
again. Wouldn't you do this anyway in the morph step? Wouldn't the
process go something like: Turn off charges -> Morph LJ parameters ->
Turn on charges.
Quoting Jussi Lehtola <[EMAIL PROTECTED]>:
> Hi,
>
>
>
> first of all, thanks to Mark and David for helping me with building
> potentials.
>
> Is there any way to speed up x2top? When I have generated a system of
> thousands of molecules using genconf and make a topology for it using
> x2top, the
Hi,
first of all, thanks to Mark and David for helping me with building
potentials.
Is there any way to speed up x2top? When I have generated a system of
thousands of molecules using genconf and make a topology for it using
x2top, the process can take hours. Is it OK just to copy the
single-mol
Hi,There can be many reasons for such problems.I assume you use solvent.One
option is that you could have made your whole proteina single charge group.
grompp in Gromacs 3.3.3 checks for this,but older versions do not.Berk.> From:
[EMAIL PROTECTED]> To: gmx-users@gromacs.org> Date: Thu, 8 May 20
Hi,
If you expect a dilute homogeneous distribution and you make an rdf between
a group and itself, it should go to 1-1/N.
But for for instance liquid water it would go to 1, since the (N-1)/N molecules
can sample the whole volume minus the volume of one molecule.
Berk.
Date: Thu, 8 May 2008 16
Thanks!
Ok, so just to be clear, should I expect my RDF to go to 1 or 1-1/N at a
sufficiently large range?
2008/5/8 Berk Hess <[EMAIL PROTECTED]>:
> Hi,
>
> The integrated rdf's never go to 1, since your box has corners which fall
> out of a sphere.
> The normalization should be ok.
> Some time
Dear all,
During my simulations of a GFP protein (force field made with amber,
then converted to gromacs), I usually get this error:
Fatal error: ci = 8108 should be in 0 .. 7937 [FILE nsgrid.c, LINE 218]
What this that means?
If I restart the simulation from the frame just before the crash
Hi,
Just a sideremark, but are you sure you want to solvate your ~6000 atom
protein in a box with nearly 3 million water molecules?
Berk.
> Date: Thu, 8 May 2008 16:04:20 +0530
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.org
> Subject: [gmx-users] Unable to neutralize my system
>
> Dear
Hi,
The integrated rdf's never go to 1, since your box has corners which fall out
of a sphere.
The normalization should be ok.
Some time ago the normalization was slightly different, g_rdf normalized with
the number
of atoms - 1, if both groups were identical. I removed this in, I think, 3.3.2.
Hello
Sorry if I address an already covered issue. I happened to notice that adding
up
the ffamber03 partial charges for ARG doesnt yield +1 but ~1.6. Also, for CYX
the total charge is ~0.87. Is this is a known issue?
In the .itp file, pdb2gmx adds up rounded charge values (as seen in the qto
Quoting [EMAIL PROTECTED]:
> Thanks for the suggestions but just to make my problem more clear
>
> The "genion" command that I used is:
>
> /opt/gromacs/bin/genion_mpi -s em.tpr -o ce_myoII_frag0_neu.gro -g
> genion.log -np 2 -pname Na+
>
> And the topology file is:
>
> Before adding ions:
>
>
Thanks for the suggestions but just to make my problem more clear
The "genion" command that I used is:
/opt/gromacs/bin/genion_mpi -s em.tpr -o ce_myoII_frag0_neu.gro -g
genion.log -np 2 -pname Na+
And the topology file is:
Before adding ions:
[ molecules ]
; Compound#mols
Protein
Quoting [EMAIL PROTECTED]:
> Dear sir,
> I want to create S-S bond between two cys in a peptide chain
> irrespective of
> the conformation of the peptide. I tried this using an option -ss as flag
> in pdb2gmx but it failed to create S-S bond. since, S-S ditance was more
> in free cysSH cysSH, b
Sorry, not Rmax (the box size) but Rmax-Rmin (box size minus size of the
molecule); still, the integrated RDF values seem to deviate from what
ithey're supposed to be...
2008/5/8 Vasilii Artyukhov <[EMAIL PROTECTED]>:
> Hi,
>
> I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecule
Quoting [EMAIL PROTECTED]:
> Dear All
>
> When I run the command "genion" specifying the number n type of chrges to
> be added, it works fine. I also have made changes in my topology file. But
> somwhow when I run the "grompp" after that it gives me the following
> error...
>
> processing topology
You haven't edited your topology files correctly. If changing the number of
ions has not resulting in a change of charge, I'd suggest you haven't added the
ions in right; otherwise, I suspect it's something to do with the number of
waters. Particularly as the error in coordinates vs. topology
Dear sir,
I want to create S-S bond between two cys in a peptide chain
irrespective of
the conformation of the peptide. I tried this using an option -ss as flag
in pdb2gmx but it failed to create S-S bond. since, S-S ditance was more
in free cysSH cysSH, but i want to bring them together to form
Dear All
When I run the command "genion" specifying the number n type of chrges to
be added, it works fine. I also have made changes in my topology file. But
somwhow when I run the "grompp" after that it gives me the following
error...
processing topology...
Generated 380 of the 1326 non-bonded p
Dear sir,
I want to create S-S bond between two cys in a peptide chain
irrespective of
the conformation of the peptide. I tried this using an option -ss as flag
in pdb2gmx but it failed to create S-S bond. since, S-S ditance was more
in free cysSH cysSH, but i want to bring them together to form
Hi Robert
Sounds familiar to me. I also tried to compute free energy differences
by letting whole bases appear/disappear. I ran into the same problems
and haven't found a solution yet. Probably the perturbation is too large
to gain converged results. My solution was stopping those simulations.
Andrea:
I believe you should simply make a script for consecutive runs.
Andrea Bortolato wrote:
> > Dear all,
> >
> > I would like to increase linearly the force constant of some distance
> constraints during my MD and then decrease it:
> >
> > 2 ps for 100 cycles with the force constant being ra
Hi,
I'm using g_rdf 3.3.3 to analyze the distribution of solvent molecules in
water. What puzzles me is that sometimes in, e.g., two sequential runs, I
get two RDF's with one of them having *uniformly* larger values than the
other. Given the fact that the RDF should in principle be normalized, thi
Bernhard Knapp wrote:
Hi there,
I wanted to ask if gromacs is able to deal correctly with peptides which
have been acetylized at the N-terminal end? if so what would be the
approbriate way (tool) to model the acetyl?
Various force fields have the acetyl group available as an N-terminal
"cap
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 there,
I wanted to ask if gromacs is able to deal correctly with peptides which
have been acetylized at the N-terminal end? if so what would be the
approbriate way (tool) to model the acetyl?
thx
Bernhard
--
Bernhard Knapp
Unit for Medical Statistics and Informatics - Section for Biomedic
Thnaks for your help Tsjerk.
One more thing I didnt understand is, if use all same commands except choosing
options in make_ndx file like " 1 | r 50-80 " generated rmsd.xvg without
issuing error, but if i use below mentioned commnands showing error, which way
is correct?
Thanks for your apprec
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 all,
1)I made make_ndx file for my protein because i want to plot rmsd for specific
residues in protein, so I have givenlike this 1 & r 50-80
2)Then I have used trjcat -f 1ns.xtc 2ns.xtc 3ns.xtc -n r_50_80.ndx -settime -o
trjout , here I selected
Protein_&_r_50-80
this command ran withou
34 matches
Mail list logo
