Thanks Justin.
-Original Message-
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Justin Lemkul
Sent: Thursday, September 26, 2013 7:51 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Membrane simulation with OPLS ff.
On 9/26
On 26 Sep, 2013, at 19:50, Justin Lemkul wrote:
> On 9/26/13 10:47 PM, Christopher Neale wrote:
>> Dear Karthi:
>>
>> As far as I am aware, there is no OPLSAA lipid force field. I have used
>> Berger lipids with OPLSAA protein
>> ( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but t
On 9/26/13 10:47 PM, Christopher Neale wrote:
Dear Karthi:
As far as I am aware, there is no OPLSAA lipid force field. I have used Berger
lipids with OPLSAA protein
( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing
a UA lipid with an AA protein
so be aware of pos
Dear Karthi:
As far as I am aware, there is no OPLSAA lipid force field. I have used Berger
lipids with OPLSAA protein
( http://www.pomeslab.com/files/lipidCombinationRules.pdf ) but that is mixing
a UA lipid with an AA protein
so be aware of possible problems arising out of that.
Charmm has pr
Dear GMX users:
Is OPLSAA forcefield data already available for POPC membranes. I am
interested in simulation of proteins in POPC membrane.
Thank you.
Best Regards
Karthi.
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On 4/18/13 10:59 AM, Giuseppe wrote:
Dear all
I'm trying to start a simulation with a protein embedded in a bilayer of
POPC molecules, but I have some problems when I pack the lipids around the
protein. Infact I place the protein in the proper position using the
editconf tool with the “-rota
Dear all
I'm trying to start a simulation with a protein embedded in a bilayer of
POPC molecules, but I have some problems when I pack the lipids around the
protein. Infact I place the protein in the proper position using the
editconf tool with the “-rotate” and “-center” options on, but when I
On 2/4/13 11:09 PM, John K wrote:
Hello Justin,
Thank you for providing a tutorial for membrane simulation.
I am doing membrane simulation by following your tutorial.
When I tried to do energy minimization after inflating the system i got the
following result.
Steepest Descents converged to m
Hello Justin,
Thank you for providing a tutorial for membrane simulation.
I am doing membrane simulation by following your tutorial.
When I tried to do energy minimization after inflating the system i got the
following result.
Steepest Descents converged to machine precision in 15 steps,
but did
On 5/3/12 10:39 AM, scapr...@uniroma3.it wrote:
Than you very much for your reply.
I'm using ffnonbonded.itp etc. I still have some doubts regarding to the
topology file which has to be used. Should I work and modify the topology
file associated with the protein by adding the information relate
Than you very much for your reply.
I'm using ffnonbonded.itp etc. I still have some doubts regarding to the
topology file which has to be used. Should I work and modify the topology
file associated with the protein by adding the information related to the
DPPC lipids as reported in the manual? I me
Von: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] Im
Auftrag von Anirban Ghosh
Gesendet: Donnerstag, 3. Mai 2012 13:39
An: Discussion list for GROMACS users
Betreff: Re: [gmx-users] membrane simulation
On Thu, May 3, 2012 at 4:38 PM,
mailto:scapr...@uniroma3.it>>
On Thu, May 3, 2012 at 4:38 PM, wrote:
> Hi all,
> I'm new in Membrane simulations with Gromacs. I have to simulate a system
> made up of a protein just leant on a membrane patch which has previously
> been extended and made it free of periodicity (with trjconv). I'm reading
> the "KALP15 in DPPC
Hi all,
I'm new in Membrane simulations with Gromacs. I have to simulate a system
made up of a protein just leant on a membrane patch which has previously
been extended and made it free of periodicity (with trjconv). I'm reading
the "KALP15 in DPPCI" Tutorial and, so far, I managed to obtain my pro
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