Dear all,
I setup a simulation system that contains a peptide and membrane. The
peptide is in water and I want to restraint the peptide to make it parallel
with the surface of the membrane. How can I achieve this goal?
If the first problem has solutions, then I have the second question is that
if
http://pubs.acs.org/doi/abs/10.1021/jp9110794
>
> Regards,
>
>
>
> On 17 May 2016 at 01:59, Khuong Truong Gia <khuon...@gmail.com> wrote:
>
> > Dear all,
> >
> > I need your help about how to check the PMF convergence. Can you guys
> show
> >
Dear Justin,
I got it. Thank you very much for your kindly reply.
Best regards,
Khuong
On Tue, Mar 29, 2016 at 6:56 PM, Justin Lemkul <jalem...@vt.edu> wrote:
>
>
> On 3/28/16 9:02 PM, Khuong Truong Gia wrote:
>
>> Dear all,
>>
>> I am running umbrel
Dear all,
I am running umbrella sampling simulation about binding of a drug (polymer)
to a lipid bilayer. Could you please suggest me how can I do
position-restraints the reference group (bilayer)? Do I need to restraint
all lipid molecules?
As I read in the gromacs manual there is cylinder
Hi all,
I am using gromacs to run umbrella sampling simulation with a drug molecule
(polymer). I got force field from PRODRG.
When run pulling the drug I got this error:
step 86530014: Water molecule starting at atom 8336 can not be settled.
Check for bad contacts and/or reduce the timestep if
Hi all,
I am using gromacs to run md simulation and I in my system I have 10
molecules of moleculetype A. I want to set position restraint for 3
molecules of moleculetype A and let 7 remained molecules relax. Can anyone
help me to archive this goal?
Thank you very much,
Khuong
--
Gromacs Users
Hi all,
I have 2 questions and I need your help:
First, I setup 2 coarse grained simulations using insane.py and
martini_v2.2. In my systems I put protein on the surface of membrane, the
first system using 1 protein and the second I use 8 protein. The first
system run normally but in the second
