On 5/06/2012 6:46 PM, Laurence Leherte wrote:
Hello,
Thank you very much for your reply. I actually carried out very basic
MDs of a peptide in vacuum (no pbc, cut-off for electrostatics and vdw
= "infinity", niter = 10^6). The computing results are given in the
two tables below. As they are
Hello,
Thank you very much for your reply. I actually carried out very basic
MDs of a peptide in vacuum (no pbc, cut-off for electrostatics and vdw =
"infinity", niter = 10^6). The computing results are given in the two
tables below. As they are identical, I am assuming that there is only
o
On 5/06/2012 12:08 AM, Laurence Leherte wrote:
Dear Gromacs users,
I am using the Amber99 FF in MD simulations of peptides (and
proteins). In a first stage to the design a different charge
distribution, most of the atomic charges were set equal to zero (i.e.,
all charges but the C and O backb
Carla Jamous wrote:
Hi everyone,
please is there a way to know if electrostatic interactions exist
between my ligand and my protein during the trajectory? Which tool can I
use for this purpose, other than g_saltbr?
You can quantify short-range nonbonded energies using energygrps, which at
On May 3, 2010, at 7:01 PM, abdullah ahmed wrote:
I wish I could use a picture :)
Unfortunately, this is not possible since I need the energy value to
be able to compare this to other mutations of the same structure and
to provide a "measure" of how energetically favourable one is in
comp
I wish I could use a picture :)
Unfortunately, this is not possible since I need the energy value to be able to
compare this to other mutations of the same structure and to provide a
"measure" of how energetically favourable one is in comparison to the other.
And I am using a box of water becau
On May 3, 2010, at 6:40 PM, abdullah ahmed wrote:
Actually I'd just like to know why both structures have such similar
coloumb energy values.
If an electro-static interaction is being made in one structure and
not in the other then their coloumb energy values should be
different too, no? W
Actually I'd just like to know why both structures have such similar coloumb
energy values.
If an electro-static interaction is being made in one structure and not in the
other then their coloumb energy values should be different too, no? Wouldn't
this be visible with simple energy minimisatio
ometry is
identical with the exception of the second charged residue, which is
replaced by Leucine in one structure.
> Date: Mon, 3 May 2010 12:11:12 -0400
> From: jalem...@vt.edu
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] electrostatic interactions
>
>
&g
abdullah ahmed wrote:
Thank you for your reply,
Settings:
I am using the procedure outline by the "speptide" tutorial (i.e.
pdb2gmx, followed by editconf, genbox, grompp, and mdrun). The ".mdp"
file I've used is as follows:
;User spoel (236)
;Wed Nov 3 17:12:44 1993
;Input fil
abdullah ahmed wrote:
Hello everyone,
I have just started using GROMACS, and apolise if my question is naive.
Basically, I'd like to ask if anyone has some suggestions regarding the
settings I should use for electrostatic interactions?
Well, you haven't shown us what settings you're usin
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