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
tem.
>
> 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:
> >
> >
emkul :
>
>
> 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 a
ation box, it goes up to
2.5 million atoms.
2016-10-13 14:40 GMT+01:00 Justin Lemkul :
>
>
> 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
with minimization and so on.
2016-10-13 14:49 GMT+01:00 Justin Lemkul :
>
>
> 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,
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.
> >
> &
Dear all,
I have a few questions regarding a simulation system containing a protein
in a box of water, with ions. Just like the lysozyme tutorial:
my system is a 5000 residue enzyme (75600 atoms), in a triclinic TIP3P
water box of a total 1567103 atoms (around 50 water molecules). My
input is
