Hi gromacs users,
I want to calculate the energy for comparative analysis of protein with and
without metal ion, wherein I would like to determine the influence of metal
on protein structural stability. I have used gromacs for simulation. Please
suggest me how to do this kind of analysis? Should i
Hello,
I am running simulations of two protein domains in tip4p water and 0.15M
salt concentration that contain up to 650,000 atoms total. The protein
domains are separated from each other at the start of each simulation and I
am measuring how the distance between them changes over time.
Now, I n
Hi,
I don't understand what you think you want long cutoffs for. They are baked
into the force field and you should not change those without reason to
believe it already works.
Mark
On Sat, 18 Nov 2017 18:08 Iman Ahmadabadi
wrote:
> Dear Gromacs Users,
>
> I need to determine the 2.0 nm for VD
Hi,
Yes those will affect what configurations are sampled, but not the LJ
component of the energy of the configurations.
Mark
On Sat, 18 Nov 2017 23:54 Alex wrote:
> And the things that affect the motion of the things with LJ interactions.
> :)
>
> Alex
>
>
> On 11/18/2017 3:49 PM, Mark Abraha
Hi,
Looks like you made a typo with state.cpt and that you perhaps have
multiple mdrun processes running such that the actual output file is in one
of the backup files labelled with # characters.
Mark
On Fri, 17 Nov 2017 19:37 Ali Ahmed wrote:
> Hello GROMACS users
> My MD simulation was crash
And the things that affect the motion of the things with LJ interactions. :)
Alex
On 11/18/2017 3:49 PM, Mark Abraham wrote:
Hi,
Only things with LJ interactions can influence the LJ energy.
Mark
On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh wrote:
I have 2 questions please. They seem eviden
Hi,
Yes, modulo any exclusions you used.
Mark
On Fri, 17 Nov 2017 18:50 Faezeh Pousaneh wrote:
> Hi,
>
> I have a simple system of non-charged diatomic molecule, (A-B).
>
> I expect total LJ interaction energy in such system when we put LJ
> parameters of atom B zero (c6 and c12=0) should be
Hi,
Only things with LJ interactions can influence the LJ energy.
Mark
On Fri, 17 Nov 2017 21:06 Faezeh Pousaneh wrote:
> I have 2 questions please. They seem evident, but I need to be sure to
> solve my simulation problem:
>
> 1- Does being a virtual site (charge, no mass) or a normal atom, e
Dear Gromacs Users,
I need to determine the 2.0 nm for VDW and Coulombic cut offs for my box
that its height along z direction is too small (for example 2.0 nm) but
the error will arise for me and I couldn't use the cut off more than 1.0 nm
because of the box size. What should I do in this regard
Hi,
I have a simple system of non-charged diatomic molecule, (A-B).
I expect total LJ interaction energy in such system when we put LJ
parameters of atom B zero (c6 and c12=0) should be equal with total LJ
energy of a system containing only atom A.
Am I right?
Best regards
--
Gromacs Users mai
Hi,
I have 2 questions please. They seem evident, but I need to be sure to
solve my simulation problem:
1- Does being a virtual site (charge, no mass) or a normal atom, effects on
its LJ interaction energies with rest of system?
2- Does adding a dummy massive site (no charge, only mass) to atom
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