On Thu, Apr 29, 2010 at 3:29 PM, Saumya wrote:
> Hi all,
>
> I am using the pre-equilibriated layers from Tieleman. After the first
> energy minimization step, I removed the periodicity using trjconv. Now, in
> order to scale the lipid positions, I tried using Inflategro.
> Do I need to use stron
Hi all,
I am using the pre-equilibriated layers from Tieleman. After the first
energy minimization step, I removed the periodicity using trjconv. Now, in
order to scale the lipid positions, I tried using Inflategro.
Do I need to use strong position restraints (because that is for protein and
I am
On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul wrote:
>
>
> Arun kumar V wrote:
>
>> Try PRODRG server to build the molecule as well as to get topology file.
>> Though you might have to be careful in using this topology file.
>>
>>
> If by "be careful" you mean "don't use this topology," I'll
Hi Saumya,
for topology please look at those two paper from Poger in which he
derive new parameters for various lipids:
1. Poger D., van Gunsteren W. F. & Mark A. E. (2009) A new force field
for simulating phosphatidylcholine bilayers. J. Comput. Chem. in press
(doi: 10.1002/jcc.21396)
2.
Arun kumar V wrote:
Try PRODRG server to build the molecule as well as to get topology file.
Though you might have to be careful in using this topology file.
If by "be careful" you mean "don't use this topology," I'll agree :) The Gromos
parameters for lipids (at least Gromos87 and Gromo
Try PRODRG server to build the molecule as well as to get topology file.
Though you might have to be careful in using this topology file.
Arun
Saumya wrote:
Hi all,
Well, I have been trying to make lipid bilayers using genconf of
gromacs from a single lipid molecule.
Can anyone tell me how t
Hi all,
Well, I have been trying to make lipid bilayers using genconf of
gromacs from a single lipid molecule.
Can anyone tell me how to proceed with the simulation of lipid
bilayers starting with a single lipid molecule?
How can I obtain the .pdb file for a lipid?
Is there any manual that describ
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