On 11/9/17 11:44 AM, Chetan Puri wrote:
Thanks for the reply,
But I could not understand what you want to say,
Since I am trying to do the ligand and membrane simulation while
constraining
the lipid
Constraints and restraints are different. My advice is to not apply any
form of *position res
Thanks for the reply,
But I could not understand what you want to say,
Since I am trying to do the ligand and membrane simulation while
constraining
the lipid
CHETAN
On 6 Nov 2017 5:24 pm, "Justin Lemkul" wrote:
>
>
> On 11/6/17 12:22 AM, Du, Yu wrote:
>
>> Hi, Justin,
>>
>> Thanks for your ques
> On 11/6/17 12:22 AM, Du, Yu wrote:
> > Hi, Justin,
> >
> > Thanks for your question. Presume that ligands were in only one side of the
> > box outside of the membrane.
> >
> > 1)In metadynamics, the membrane will be pushed by the ligands. After long
> > time simulation, the membrane may move a
On 11/6/17 12:22 AM, Du, Yu wrote:
Hi, Justin,
Thanks for your question. Presume that ligands were in only one side of the box
outside of the membrane.
1)In metadynamics, the membrane will be pushed by the ligands. After long time
simulation, the membrane may move along the Z-axis.
2)In st
2017-11-06 01:14:22 (Monday)
> To: gmx-us...@gromacs.org
> Cc:
> Subject: Re: [gmx-users] Determining a ligands permeability
>
>
>
> On 11/5/17 7:40 AM, Du, Yu wrote:
> > Hi,
> >
> > I don't study the membrane permeability of small molecules and can&#x
On 11/5/17 7:40 AM, Du, Yu wrote:
Hi,
I don't study the membrane permeability of small molecules and can't give
related papers.
All in all, you need to first successfully simulate the lipid-small molecule
system and then enhanced sampling because of the time scale of ligand diffusing
acros
-05 19:39:47 (Sunday)
> To: gmx-us...@gromacs.org
> Cc:
> Subject: [gmx-users] Determining a ligands permeability
>
> I have tried to do an umbrella sampling for a ligand (drug) and membrane as
> per the gromacs tutorial. Now i want to calculate permeability and
> diffusibilit
I have tried to do an umbrella sampling for a ligand (drug) and membrane as
per the gromacs tutorial. Now i want to calculate permeability and
diffusibility for this ligand, so can anyone suggest how to proceed further.
Since there is some literature available but it does not show the proper
method
