Thanks for your response.
Actually I fully followed your tutorial. the pull-coord1-rate = 0.007
indicated in the pdf file is just for the pulling step and then in the next
step I have pull-coord1-rate = 0.0 for each windows. Can we do the pulling
step with pull-coord1-rate = 0.0 !?
Regards,
Alex
Hi,
my name is Matilde. This is my first time using GROMACS. I'm switching from
AMBER to GROMACS however I'm having some trouble reproducing my system:
In AMBER, I'm working with a 5000 residues protein, a water box (TIP3) of
12A, roughly 1.5 million atoms total. I tried building the same system
You can reduce your box size to get a smaller system.
On 13 October 2016 at 17:41, Matilde Viegas
wrote:
> Hi,
>
> my name is Matilde. This is my first time using GROMACS. I'm switching from
> AMBER to GROMACS however I'm having some trouble reproducing my system:
>
> In AMBER, I'm working with
I tried to downzise to 10 and yet the reduction was very little. I was just
trying t understand how can the difference between the same systems, using
either AMBER or GROMACS, can be of 1 million atoms...
2016-10-13 12:27 GMT+01:00 Dd H :
> You can reduce your box size to get a smaller system.
>
Dear all,
I will use Gromacs to calculate the chemical potential difference of solvation
a surfactant molecule on the surface.
System covers water molecules covered with surfactant molecules.
I will apply flat-bottom restraint to the surfactant molecules in order to
stabilise them on surface. I
On 10/13/16 7:34 AM, Matilde Viegas wrote:
I tried to downzise to 10 and yet the reduction was very little. I was just
trying t understand how can the difference between the same systems, using
either AMBER or GROMACS, can be of 1 million atoms...
GROMACS uses SI units, so distances/box vect
On 10/12/16 11:06 PM, Dd H wrote:
I found these words in the GROMACS v4.5.5 manual:
*[ atoms ] : defines the molecule, where nr and type are fixed, the rest is
user defined. So*
*atom can be named as you like, cgnr made larger or smaller (if possible,
the total charge of a **charge group shoul
On 10/13/16 5:28 AM, Alex wrote:
Thanks for your response.
Actually I fully followed your tutorial. the pull-coord1-rate = 0.007
indicated in the pdf file is just for the pulling step and then in the next
step I have pull-coord1-rate = 0.0 for each windows. Can we do the pulling
step with pul
Thank you so much!
On 13 October 2016 at 20:07, Justin Lemkul wrote:
>
>
> On 10/12/16 11:06 PM, Dd H wrote:
>
>> I found these words in the GROMACS v4.5.5 manual:
>>
>> *[ atoms ] : defines the molecule, where nr and type are fixed, the rest
>> is
>> user defined. So*
>> *atom can be named as y
The negative and positive in the the reaction coordinate comes probably
from interaction of peptide with surface in bottom slab and top(next cell
beacuse of PBC) slab in the Z direction.
But I was always taking care about sampled windows so that the peptide
pulled away from top of bottom surface to
Dear gromacs user,
As you know the binding free energy is the difference between the free
energy change inbounded state and unbounded state.
\Delta (\Delta G)_(binding) = \Delta G_(bounded) - \Delta G_(unbounded).
Then my question is that if it is necessary to simulate the free energy
change of
Yes, I noticed that! I said 10, referring to angstrom, in the input I had
1.0nm.
So you probably think it is only some error in the input, not really
something I can tackle, right? I really can't figure it out...
Thank you for your time, Justin
2016-10-13 13:04 GMT+01:00 Justin Lemkul :
>
>
> O
On 10/13/16 9:38 AM, Matilde Viegas wrote:
Yes, I noticed that! I said 10, referring to angstrom, in the input I had
1.0nm.
So you probably think it is only some error in the input, not really
something I can tackle, right? I really can't figure it out...
Without seeing your exact sequence
Dear all,
I will use Gromacs to calculate the chemical potential difference of solvation
a surfactant molecule on the surface.
System covers water molecules covered with surfactant molecules.
I will apply flat-bottom restraint to the surfactant molecules in order to
stabilise them on surface. I
Of course, sorry!
I followed your lyzosyme tutorial, the exact same commands, only addapting
it to my system (force field, tip3p water, just like I did on AMBER), box
was dodechaedron, 1.2nm. I didn't alter anything beside that... My enzyme
is around 72 thousand atoms, after adding the solvation bo
On 10/13/16 9:45 AM, Matilde Viegas wrote:
Of course, sorry!
I followed your lyzosyme tutorial, the exact same commands, only addapting
it to my system (force field, tip3p water, just like I did on AMBER), box
was dodechaedron, 1.2nm. I didn't alter anything beside that... My enzyme
is around 7
Hi Everyone,
I have extended my simulation from 6 ns to 20 ns. Now I want to rerun to
calculate energy between various energy groups. I have 2 xtc files one
having first 6ns and one with 14 ns (7th to 20th) (Even though I used
append during mdrun). My doubts are:
1) What will be the mdp option for
On 10/13/16 9:50 AM, Tushar Ranjan Moharana wrote:
Hi Everyone,
I have extended my simulation from 6 ns to 20 ns. Now I want to rerun to
calculate energy between various energy groups. I have 2 xtc files one
having first 6ns and one with 14 ns (7th to 20th) (Even though I used
append during mdr
I started with a pdb file of the protein, 5000 residues, no solvent,
crystallographic structure.
Generated the .gro file, opting for the AMBER99SB force field (option 5):
gmx pdb2gmx -f YYY.pdb -o YYY_GROMACS.gro -water tip3p -ignh (opted
for ignh as I was having trouble with differences in nomem
Hi,
Do check out gmx editconf -h for what it says about -d. Hint, that isn't
setting the box dimensions directly, which is why you're getting a much
bigger box. Look also at the output of editconf, which will tel lyou that
it's too big.
Mark
On Thu, Oct 13, 2016 at 4:39 PM Matilde Viegas
wrote
Thank you Mark, will look into that!
2016-10-13 15:45 GMT+01:00 Mark Abraham :
> Hi,
>
> Do check out gmx editconf -h for what it says about -d. Hint, that isn't
> setting the box dimensions directly, which is why you're getting a much
> bigger box. Look also at the output of editconf, which wil
You probably want to use -box 1.2 1.2 1.2 rather than -d 1.2.
Best wishes
James
> Thank you Mark, will look into that!
>
> 2016-10-13 15:45 GMT+01:00 Mark Abraham :
>
>> Hi,
>>
>> Do check out gmx editconf -h for what it says about -d. Hint, that isn't
>> setting the box dimensions directly, whic
What are the box dimensions (at the end of the gro file)?
Any chance you are mixing Ångström (default in Amber) and nanometer
(default in GROMACS)?
Best,
Stéphane
Le 13/10/2016 à 13:34, Matilde Viegas a écrit :
I tried to downzise to 10 and yet the reduction was very little. I was just
try
23 matches
Mail list logo
