Dear gmxers,
I am puzzling about the gbsa.itp file as listed below. What does each
item mean? Could you please explain it?
;atype sar st pi gbr hct
opls_102 0.16 1 1.215 0.1625 0.79 ; N (RNH3+)
Yours sincerely,
Chaofu Wu
--
gmx-users mailing list
Dear Sir / Madam,
I want run Solvent accessible surface area in
gromacs,i aware about g_sas is there but for selecting group little bit
confusing
Reading frame 0 time0.000 Select a group for calculation of
surface and a group for output:
Group 0 (
> 1) That .mdp applies different tables to K-K, protein-protein and all
> other interactions, which isn't what you've said you've done.
> 3) Your life will be simpler if you use energygrp_table only for the
> group-group interactions you want to change, and leave the default
> interactions nor
On 9/2/12 2:10 PM, venkatesh s wrote:
Dear Sir / Madam,
I want run Solvent accessible surface area in
gromacs,i aware about g_sas is there but for selecting group little bit
confusing
Reading frame 0 time0.000 Select a group for calculation of
surface and
On 9/2/12 5:14 AM, Wu Chaofu wrote:
Dear gmxers,
I am puzzling about the gbsa.itp file as listed below. What does each
item mean? Could you please explain it?
;atype sar st pi gbr hct
opls_102 0.16 1 1.215 0.1625 0.79 ; N (RNH3+)
Manual sectio
On 9/1/12 3:38 PM, fatemeh ramezani wrote:
Dear gromacs users
I want to simulate gold nanoparticle by golp force field that needs to
determine virtual sites for Au atoms. I read gromacs manual section 5.2.2 and
4.7
but it is not clear that how can I do it and .also I read virtual site tuto
On 8/31/12 10:43 PM, Rajiv Gandhi wrote:
Can you tell me "how to predict the Hydrogen bond breaking process (For
example Fe-CO hydrogen bond broken in Myoglobin at 100 ps) through MD
simulation?
There is no hydrogen bonding in a Fe-CO interaction. That is a coordinate
covalent bond. If yo
Could you tell me how can i perform for coordinate covalent bond breaking
and forming between Fe-CO in myoglobin. I guess, it has been already done
by some groups. If possible can you send me journals related to this.
Thanks.
On Mon, Sep 3, 2012 at 8:55 AM, Justin Lemkul wrote:
>
>
> On 8/31/12
On 9/2/12 9:42 PM, Rajiv Gandhi wrote:
Could you tell me how can i perform for coordinate covalent bond breaking
and forming between Fe-CO in myoglobin. I guess, it has been already done
by some groups. If possible can you send me journals related to this.
You can't break and form bonds in cl
Well there is always ReaxFF. You'd still have to use QM/MM to parameterize
the various states though.
On 2012-09-02 09:48:25PM -0400, Justin Lemkul wrote:
>
>
> On 9/2/12 9:42 PM, Rajiv Gandhi wrote:
> > Could you tell me how can i perform for coordinate covalent bond breaking
> > and forming b
Is there any publication regarding this Fe-CO covalent bond breaking ?
Actually in experimental techniques, the bond between Fe-CO in myoglobin
gets broken in100 ps time scale. Is't possible to do this process by QM/MM
methods or ReaxFF? Please need an advice. I haven't have any
prior knowledge on
hi all,
I would like to measure the hydrophobic interaction of the ligand against
the protein during the simulation . From the forum I learnt g_mindist will
be the better tool. But when i used the command g_mindist -f traj.xtc -s
topol.tpr -n index.ndx -on numcont.xvg -group and selected protein
Thanks for your response, but
I've read the manual. What I realized is that, for example, I should consider
for every two, three or … atoms, a virtual atom. Here are some questions:
1 - Does not important consider which atoms together? or How much is the angle
between atoms?
2 -Does I need t
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