Hi all,
During my MD the molecule experience a drift. Now I want to put the
molecule at the center of the water box.
I tried with trjconv using the -pbc mol and -center flag and using a
reference frame where the molecule is at the center of the box.
It seems that all the box (water+molecule) i
Dear Users.
Greetings. Please someone can tell me how can I proceed
to save all MD snapshot for a long time simulation
after equilibration.
Thanks a lot for all.
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Collins Nganou skrev:
Dear Users.
Greetings. Please someone can tell me how can I proceed
to save all MD snapshot for a long time simulation
after equilibration.
You can set the parameters below to the value "1" in the configuration
file for mdrun.
nstxout = 1
nstvout = 1
nstfout = 1
/And
The snapshots are saved automatically during the simulation in the trajectory,
e.g.
mdrun ... -x trajectory.xtc
How often snapshots are saved depends on the settings in your .mdp-file.
I recommend some reading of the manual before starting any simulations.
Regards
Andreas
From: [EMAIL PR
h a wrote:
Dear users,
I'm working on simulating protein interactions with polymer surface for
tissue engineering applications.
I have developed a primitive model of polymer surface of polystyrene using
"genconf". I have obtained .gro and .itp files using prodrg. But now I
face error when I
On Tuesday 01 July 2008 10:17, Fabio Affinito wrote:
if you have only one molecule in the box, and you are equilibrated, why would
your molecule move around?
A visualization problem? Can you center it with editconf maybe?
Peyman
> Hi all,
> During my MD the molecule experience a drift. Now I wa
On Tuesday 01 July 2008 07:48, h a wrote:
what is the error?
> Dear users,
>
> I'm working on simulating protein interactions with polymer surface for
> tissue engineering applications.
>
> I have developed a primitive model of polymer surface of polystyrene using
> "genconf". I have obtained .gr
What box type are you using? Try adding following options
-center -pbc mol -ur compact
kind regards,
servaas
Hi all,
During my MD the molecule experience a drift. Now I want to put the
molecule at the center of the water box.
I tried with trjconv using the -pbc mol and -center flag and u
The protein experience self-diffusion and so it moves through the
simulation box.
I tried also with editconf but the result is the same.
F.
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Please
Fabio Affinito wrote:
Hi all,
During my MD the molecule experience a drift. Now I want to put the
molecule at the center of the water box.
I tried with trjconv using the -pbc mol and -center flag and using a
reference frame where the molecule is at the center of the box.
It seems that all the
I choosed "Protein" for centering and "System" for output.
Same stuff with editconf.
F.
Fabio Affinito, PhD
email: [EMAIL PROTECTED] phone:+39 040 3787 303 fax:+39 040 3787 528
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On Tuesday 01 July 2008 12:24, Fabio Affinito wrote:
I think if it moves, then there is something more basic wrong, do you remove
your center of mass motion appropriately? is your box homogeneously
equilibrated? but if it does not move and it looks like as if it moved, then
it's visual problem
Peyman,
the protein moves because the c.o.m. motion wasn't subtracted during
the dynamics.
On Tuesday 01 July 2008 12:24, Fabio Affinito wrote:
I think if it moves, then there is something more basic wrong, do
you remove
your center of mass motion appropriately? is your box homogeneousl
Dear All,
I'm looking for gromacs parameters for heme bound to oxygen
molecule . I will appreciate getting the parameters or any tip
considering the best way to create them.
Thank you
Rotem Sertchook
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Dear Gromacs USERs,
My ligand, which contains a piperazine ring & needs to be positively charged
(+1).
When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen.
But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733
on this atom. So does it mean it has
If they are not among the user contributions, and if they are not
published somewhere in the literature, you will have to derive them
yourself (an advanced topic!). See here:
http://wiki.gromacs.org/index.php/Parameterization
And this one is probably applicable in your case, as well:
http://
nahren manuel wrote:
Dear Gromacs USERs,
My ligand, which contains a piperazine ring & needs to be positively
charged (+1).
When I assign Gasteiger charges, it comes out to be -0.336 on the
Nitrogen.
But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it
puts +0.733 on this
Dear users,
Thanks a lot to Justin and a few others who really helped me in successfully
running insulin. Now, I am trying to setup the input file for insulin with
other enzyme and I am trying to merge the two chains of insulin. I am using
the following command:
pdb2gmx -f insu.pdb -p insu_p.top
The whole story continues to emerge... :-)
You're probably experiencing this problem because you're trying to
process two separate proteins with one pdb2gmx command. You will need
to separate (i.e., using a text editor) chain A (whatever protein) from
B&C (insulin). Process them separately w
Hello,
trying to implement my force field into gromacs I have figured out that it is
of vital importance to use diferrent cut-offs among different kind of atoms.
I have 1-4 and 1-5 interactions with a set of epsilon and sigma parameters and
the non bonded interactions (more than 4 bonds appart
Hello,
I am having trouble analyzing the XXX.pdo file output from my mdrun simulation
using the g_wham command. Specifically, my command entered is:
g_wham pull.pdo -o pull1.xvg
The error given is:
Opening file pull.pdo
_
Program g_wham, VERS
I remember that at least for the old version of g_wham, you need to gzip the
pdo files first.
Lanyuan Lu
> Date: Tue, 1 Jul 2008 11:38:18 -0400
> To: gmx-users@gromacs.org
> From: [EMAIL PROTECTED]
> Subject: [gmx-users] g_wham command issues
>
> Hello,
>
> I a
Hi all,
I have embedded protein into POPC bilayer, I accomplished energy
minimisation
em.mdp file
cpp = /usr/bin/cpp
define = -DFLEXIBLE
constraints = none
integrator = steep
nsteps = 500
; Energy minimizing stuff
;
minnale wrote:
So I dont boughter about those sentences because I confirmed in list
archives that I can proceed further steps and moreover em.gro file is
fine, so I went for restrain, here I am getting abnormal POPC
structure
means POPC tails are tilting, water molecules structure
HI
I use mk_angndx to produce angle.ndx
then, enter g_angle -od angdist.xvg -ov angaver.xvg -type dihedral
it follows the options:
Group 0 (Phi=180.0_2_70) has 4 elements
Group 1 (Phi=180.0_2_6) has16 elements
Group 2 (Phi=180.0_2_40) has 192 elements
Select a
Chih-Ying Lin wrote:
HI
I use mk_angndx to produce angle.ndx
then, enter g_angle -od angdist.xvg -ov angaver.xvg -type dihedral
it follows the options:
Group 0 (Phi=180.0_2_70) has 4 elements
Group 1 (Phi=180.0_2_6) has16 elements
Group 2 (Phi=180.0_2_40) has
Dear all,
I have some questions concerning the usage of tables :
1. If one choose ' coloumbtype = User ' then GROMACS would calculate
only the interaction according to the user specfied table within the
specified cut off 'rcoloumb' and 'rlist'. The interaction beyond the cut
offs would not
I've also tried to gzip the files, and subsequently use the same command line
as below with the zipped file. Same problem. Any other ideas?
On Tue, Jul 1, 2008 12:12 PM, LuLanyuan <[EMAIL PROTECTED]> wrote:
>
I remember that at least for the old version of g_wham, you need to gzip the
>pdo files
Thanks to Justin for comment about my problem
I will tell you clearly
1. Initially POPC bilayer taken from Tieleman website and run the simulation
for 5ns.
2. Protein also has taken and simulated for 9ns actually this contain 10
helices among that 10 helices two helices have taken, because i
HI
I have read the manual but the thing is that I could not get the
answers from the manuals. So, I repeatly ask the same questions and
if anyone could give me the exact answers. Thanks a lot.
Lin
I use mk_angndx to produce angle.ndx
then, enter g_angle -od angdist.xvg -ov anga
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