On 11/11/17 16:44, Dan Gil wrote:
Hi,
Just wanted to see if anyone had any thoughts...
For more information, if I use:
wall-ewald-zfac = 3
E-z= 1 5 0
The electric field from ionic liquid has a magnitude of 7.5 V/nm in the
opposite direction to the applied electric field.
Hi,
Let me take that in reverse order:
>
> Note that choosing appropriate atoms to apply restraints is not a trivial
> matter, and results can vary depending on the choices made.
>
I know.
I doubt there's a bug. I tested this feature a lot myself and have used it.
> How different are the
I am working on MD simulation while using Gromacs. I want to simulate
acetylated protein with DNA. Which type of force field I have to use that
encompass both DNA and acetylated histones parameters.
Regards
Najam
QAU, Pakistan.
Sent from Mail for Windows 10
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Gromacs Users mailing list
Dear Gromacs Users,
Thank you very much.
On Mon, Nov 13, 2017 at 9:56 AM, Justin Lemkul wrote:
>
>
> On 11/12/17 5:51 PM, Amali Guruge wrote:
>
>> Dear Gromacs users,
>>
>> I tried to simulate a system which contains PEG and water. According to
>> the
>> phase diagram of PEG,
On 11/12/17 5:51 PM, Amali Guruge wrote:
Dear Gromacs users,
I tried to simulate a system which contains PEG and water. According to the
phase diagram of PEG, it should form micells after the simulation. However,
after the simulation PEG doesn't form micells. What could be the reason for
On 11/10/17 11:59 PM, Ahmet Yildirim wrote:
Hi,
Just tested it. The [ dihedral_restraints ] didn't help. The RMSD of the
ligand is the same when the [ dihedral_restraints ] or [ dihedrals ] is
used at end of the complex topology file. This is a bug?
I doubt there's a bug. I tested this
You used the incorrect forcefield.
We have found that GROMOS53a6 and associated forcefields reproduce
poorly the interactions between PEG and water. We have made
improvements on that, and will be publishing something soon.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Dear Gromacs users,
I tried to simulate a system which contains PEG and water. According to the
phase diagram of PEG, it should form micells after the simulation. However,
after the simulation PEG doesn't form micells. What could be the reason for
this. Can anyone help me.
Thank you.
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Gromacs