Hi Justin,
No problem. Thanks for the clarification. I think I understand now.
Best,
Eric
On Sat, Jul 28, 2018 at 6:39 PM, Justin Lemkul wrote:
>
>
> On 7/28/18 8:35 PM, Eric Smoll wrote:
>
>> Justin,
>>
>> Thank you for the guidance.
>>
>> "You simply supply whatever the LJ combination shou
On 7/28/18 8:35 PM, Eric Smoll wrote:
Justin,
Thank you for the guidance.
"You simply supply whatever the LJ combination should be for the 1-4 pair.
If you want 0.5 times what is listed, change the values."
But this would change the LJ interaction for 1-4 pairs and all other pairs
that are
Justin,
Thank you for the guidance.
"You simply supply whatever the LJ combination should be for the 1-4 pair.
If you want 0.5 times what is listed, change the values."
But this would change the LJ interaction for 1-4 pairs and all other pairs
that are not excluded, correct? Consider a UA model
On 7/28/18 7:19 PM, Eric Smoll wrote:
On Sat, Jul 28, 2018 at 2:17 PM, Justin Lemkul wrote:
On 7/26/18 5:52 PM, Eric Smoll wrote:
Hello GROMACS users,
I have a quick question about the nonbond_params directive.
If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive,
GROMA
On Sat, Jul 28, 2018 at 2:17 PM, Justin Lemkul wrote:
>
>
> On 7/26/18 5:52 PM, Eric Smoll wrote:
>
>> Hello GROMACS users,
>>
>> I have a quick question about the nonbond_params directive.
>>
>> If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive,
>> GROMACS will
>>
>
> That's f
I do, I most definitely do. :-)
On Jul 28, 2018 2:34 PM, "Justin Lemkul" wrote:
On 7/28/18 3:21 PM, Alex wrote:
> For calculating energy barriers in a reasonably accurate way, you
> should use the potential of mean force approach (here's Justin's
> tutorial:
>
http://www.bevanlab.biochem.vt.ed
Alex,
NPT appears to be doing exactly what it should esp if your slab is a membrane
1) are you using pcoupltype = surface tension with compressability = 4.5e-5
0 ??
2) have your tried xy restraints on the ends of the slab
Paul
> On Jul 28, 2018, at 5:10 AM, Alex wrote:
>
> Dear a
On 7/26/18 5:52 PM, Eric Smoll wrote:
Hello GROMACS users,
I have a quick question about the nonbond_params directive.
If I provide gen-pairs=yes and fudgeQQ=0.5 in the defaults directive,
GROMACS will
That's fudgeLJ, not fudgeQQ, but yes.
(1) compute VDW parameters for all atomtype-pair
On 7/28/18 3:21 PM, Alex wrote:
For calculating energy barriers in a reasonably accurate way, you
should use the potential of mean force approach (here's Justin's
tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html).
I think you mea
For calculating energy barriers in a reasonably accurate way, you should
use the potential of mean force approach (here's Justin's tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/01_theory.html).
Alex
On 7/28/2018 12:57 PM, kordza...@aut.ac.ir wrot
Hi all
I 've translocated drug molecule into the different carbon nanotubes in a
pulling simulation and the force was obtained , can I tell that the case that
has maximum difference force at CNT end, has minimum energy barrier?
In real I can't find relationship between this force and energy barr
Hi all
I am performing a simulation between a protein and Fluorine molecule. I
have optimized the F2 structure using Gaussian and inserted into the box
using gmx insert-molecules command after adding solvent [gmx solvate]. The
topology for fluorine molecule is generated by topolgen.
Dear all,
In modelling a slab and some molecules on top of it, the slab gets bended
(Fig.2) during the NVT production or equilibration simulations while I do
NpT equilibration (berendsen followed by Parrinello-Rahman) long enough
(Fig.1) so that the box parameters, pressure and energies are stable
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