Dear collegues
Thank for advices. Indeed Gromacs is able to analyse two trajectories
with g_rms ( with the flags -f and -f2 ) but as the result I've obtain
graph with one rmsd plot so I'm not sure about implementation of that
method.
So I think that the algorithm proposed by Justin was exactly
Dear:
I am using command:
g_saltbr -f md.trr -s tuned.tpr -dt 16800
to calculate the saltbr and I found the output is really large:
ls -lt *.xvg
-rw-r--r-- 1 albert users 640869568 Sep 21 09:53 min-min.xvg
-rw-r--r-- 1 albert users 2392154038 Sep 21 09:53 plus-min.xvg
-rw-r--r-- 1 albert
Hi,
because g_saltbr calculates the data regarding any charge-charge
interaction ( neg neg, neg pos, pos pos).
Small problem: every atoms (C,H,S,P...) has a charge so the outputs
contains the distances among al the
n*(n-1)/2 atom couples
Francesco
2012/9/21 Albert mailmd2...@gmail.com
Hi,
2012/9/21 James Starlight jmsstarli...@gmail.com
Dear collegues
Thank for advices. Indeed Gromacs is able to analyse two trajectories
with g_rms ( with the flags -f and -f2 ) but as the result I've obtain
graph with one rmsd plot so I'm not sure about implementation of that
method.
Hi,
could you try to use the Morse potential for this bond.
As far as I know, the parameters can be directly obatined forml the armonic
potential expression.
Francesco
2012/9/21 Mark Abraham mark.abra...@anu.edu.au
On 21/09/2012 11:35 AM, Rajiv Gandhi wrote:
Dear all gromacs users,
In
Peter C. Lai wrote
Generally it's probably not a good idea to rely on tutorials designed
around 3.3 when a google search for gromacs tutorial shows a series of
4.5.x
tutorials written by Justin himself, with explanations of why certain
steps
are conducted. (also when certain features may
On 09/21/2012 10:48 AM, francesco oteri wrote:
Hi,
because g_saltbr calculates the data regarding any charge-charge
interaction ( neg neg, neg pos, pos pos).
Small problem: every atoms (C,H,S,P...) has a charge so the outputs
contains the distances among al the
n*(n-1)/2 atom couples
You should modify g_saltbr code.
Alternativley, you can create a fake .top file where charge are 0 except on
carged groups (i.e. carboxylic atoms) that are supposed to interact.
This new .top file can be used to have a new .tpr where only the
interesting atoms
are charged and are detected by
On 9/21/12 2:11 AM, James Starlight wrote:
Dear collegues
Thank for advices. Indeed Gromacs is able to analyse two trajectories
with g_rms ( with the flags -f and -f2 ) but as the result I've obtain
graph with one rmsd plot so I'm not sure about implementation of that
method.
So I think that
On 9/21/12 5:49 AM, francesco oteri wrote:
You should modify g_saltbr code.
Alternativley, you can create a fake .top file where charge are 0 except on
carged groups (i.e. carboxylic atoms) that are supposed to interact.
This new .top file can be used to have a new .tpr where only the
Dear gmx users,
We recently got a problem with the rerun feature of mdrun, and we request
your help in order to help to solve it.
We have run a simulation of a large POPC membrane using the coarse grained
Martini force fields. From these simulations we obtained a trr trajectory
file which
On 9/21/12 8:29 AM, Bastien Loubet wrote:
Dear gmx users,
We recently got a problem with the rerun feature of mdrun, and we request
your help in order to help to solve it.
We have run a simulation of a large POPC membrane using the coarse grained
Martini force fields. From these simulations
Justin Lemkul wrote
On 9/21/12 8:29 AM, Bastien Loubet wrote:
Dear gmx users,
We recently got a problem with the rerun feature of mdrun, and we request
your help in order to help to solve it.
We have run a simulation of a large POPC membrane using the coarse
grained
Martini force fields.
Desr Gromacs Users,
I have several systems consist of: surfactants, solvent, and additives
molecules in several concentrations. I want obtain extent of movement each of
materials in the mixture in different concentrations. Is the self-diffusion
coefficient good foe this? I have doubt about
Hello
My equilibration of water around lumiflavin works (I got no error, no warning
and no note). Sadly the mdrun fails with following error:
step 886: Water molecule starting at atom 7596 can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
What does GROMACS
genion does that. Sort of.
Erik
21 sep 2012 kl. 15.37 skrev Ali Alizadeh:
Dear All users
How can i select randomly some of my molecules in my box (in .gro file) and
replace them by some of other molecules?
Sincerely
--
gmx-users mailing listgmx-users@gromacs.org
On 9/21/12 9:45 AM, Lara Bunte wrote:
Hello
My equilibration of water around lumiflavin works (I got no error, no warning
and no note). Sadly the mdrun fails with following error:
step 886: Water molecule starting at atom 7596 can not be settled.
Check for bad contacts and/or reduce the
Dear users and admins,
I'm trying to use GridMAT to get the area per lipid and thickness.
To do so I ran this command:
# perl GridMAT-MD.pl param_example
It doesn't give me any valuable output. This error comes out:
Generating the grid...
Your system is bigger in the X-direction
There are 20
On 9/21/12 11:16 AM, Shima Arasteh wrote:
Dear users and admins,
I'm trying to use GridMAT to get the area per lipid and thickness.
To do so I ran this command:
# perl GridMAT-MD.pl param_example
It doesn't give me any valuable output. This error comes out:
Generating the grid...
Your
On 9/21/12 10:49 AM, Hossein Lanjanian wrote:
Dear all
I want to simulate insulin receptor in plasma membrane. The monomer form of
receptor, that has 1382 amino acid, is available in Uniprot database. But I
need dimer form of it.
question: How can I prepare a pdb file of dimer? Is there any
Hi Justin
Sorry but I don't understand what you mean with Despite being given the
correct settings for CHARMM27, you're still not using
them. I use exactly the settings Peter gave me in my last question. What is in
this settings wrong and where could I find the right settings?
Greetings
Lara
On 9/21/12 11:26 AM, Lara Bunte wrote:
Hi Justin
Sorry but I don't understand what you mean with Despite being given the
correct settings for CHARMM27, you're still not using
them. I use exactly the settings Peter gave me in my last question. What is in
this settings wrong and where could I
Thanks
justin
On Sep 21, 2012 6:53 PM, Justin Lemkul jalem...@vt.edu wrote:
On 9/21/12 10:49 AM, Hossein Lanjanian wrote:
Dear all
I want to simulate insulin receptor in plasma membrane. The monomer form
of
receptor, that has 1382 amino acid, is available in Uniprot database. But
I
need
Hi Justin
I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with
this settings grompp gives me two notes and one of this notes is inconsistent:
NOTE 1 [file pr.mdp]:
For energy conservation with switch/shift potentials, rlist should be 0.1
to 0.3 nm larger than
On 9/21/12 2:33 PM, James Starlight wrote:
Dear Gromacs Users!
In some recent publications about protein dynamics investigation I've
found reference about new gromos force field (56A7) where some fix in
case of dihedral terms have been included.
During my simulation performed with the 56A6
On 9/21/12 1:31 PM, Lara Bunte wrote:
Hi Justin
I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and with
this settings grompp gives me two notes and one of this notes is inconsistent:
NOTE 1 [file pr.mdp]:
For energy conservation with switch/shift potentials, rlist
On 2012-09-21 02:59:17PM -0400, Justin Lemkul wrote:
On 9/21/12 1:31 PM, Lara Bunte wrote:
Hi Justin
I used this settings except of vdw-type = switch and rvdw_switch = 0.8 and
with this settings grompp gives me two notes and one of this notes is
inconsistent:
NOTE 1 [file
Perhaps genion is not removing the dummy atoms properly?
On 2012-09-21 04:48:37PM +0100, Ankita naithani wrote:
Hi all,
I am trying to begin a simulation of a protein.
I am using AMBER99sb-ILDN force field and TIP4P water model. However,
I am facing a problem in the ion adding step.
On 9/21/12 7:55 PM, Peter C. Lai wrote:
Perhaps genion is not removing the dummy atoms properly?
The problem is occurring with grompp before genion. We would need to see all
the prior commands (exactly copied and pasted from the terminal) as well as the
[molecules] section of the
Dear Justin Thank you for your Reply
After pdb2gmx When i Visualize the resultant .gro file of my cyclic peptide
in VMD
I have Observed the Bond Between Nitrogen atom (N ) of First residue and
Carbon atom (C) of Last residue I have not observed The same bond when I open
and Visualize
Molecular visualization programs determine bonds through distance
measurements. Especially since .gro files do not contain connectivity
information. The topology is where the bond infomration is stored.
So check there...
On 2012-09-22 12:33:31PM +0800, vidhya sankar wrote:
Dear Justin Thank
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