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
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
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
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
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
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
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 9:38 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
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 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
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.
>
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
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