On 12/25/12 2:42 AM, Shima Arasteh wrote:
Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the
Justin's tutorial of Kalp15-DPPC.
I get the system-solved-ion.gro and run energy minimization. I saw some water
molecules in em.gro file, therefore, I erase them
: Re: [gmx-users] protein membrane system
On 12/25/12 2:42 AM, Shima Arasteh wrote:
Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the
Justin's tutorial of Kalp15-DPPC.
I get the system-solved-ion.gro and run energy minimization. I saw some water
On 12/25/12 12:53 PM, Shima Arasteh wrote:
In order to compare the first and the second .gro file, I used grep -c OW
(file.gro) to see how many waters exist in my new system. I got 22352, however
I got 23703 before ( when I had not deleted the disturbing water molecules). So
Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the
Justin's tutorial of Kalp15-DPPC.
I get the system-solved-ion.gro and run energy minimization. I saw some water
molecules in em.gro file, therefore, I erase them and then again save the .gro
file as a new
Hi all,
I'm trying to simulate a system of POPC- Protein- Water- Ion following the
Justin's tutorial of Kalp15-DPPC.
I get the system-solved-ion.gro and run energy minimization. I saw some water
molecules in em.gro file, therefore, I erase them and then again save the .gro
file as a new
*From:* Itamar Kass itamar.k...@monash.edu
*To:* Discussion list for GROMACS users gmx-users@gromacs.org
*Sent:* Thursday, 17 February 2011 07:20:19
*Subject:* Re: [gmx-users] Protein-membrane system
Dear Aldo,
It is totally OK to see water molecules within the bilayer, both
Aldo Segura wrote:
Dear gmx-users,
I completed a MD (10 ns) of my protein-membrane system. When I perform a
visual inspection (VMD) of md_0_1.gro file I observed a few water
molecules within the bilayer. In previous steps (e.g. equilibration)
this was not observed. Could be expected such
Dear Aldo,
It is totally OK to see water molecules within the bilayer, both in
simulations and real life. If I am not totally wrong, 3000 water
molecule per lipids per second are being transferred across the bilayer
without any protein involvement.
If your system is stable, the lipids
From: Itamar Kass itamar.k...@monash.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Thursday, 17 February 2011 07:20:19
Subject: Re: [gmx-users] Protein-membrane system
Dear Aldo,
It is totally OK to see water molecules within the bilayer, both in simulations
and real
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