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
23703-22352=13
es by VMD.
Any body helps me please?
I would appreciate you.
Sincerely
Shima
- Original Message -
From: Justin Lemkul
To: Shima Arasteh ; Discussion list for GROMACS
users
Cc:
Sent: Tuesday, December 25, 2012 4:56 PM
Subject: Re: [gmx-users] protein membrane system
On 12/25/12 2:
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 a
egards,
Jianguo
*From:* Itamar Kass
*To:* Discussion list for GROMACS users
*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 rea
s,
Jianguo
From: Itamar Kass
To: Discussion list for GROMACS users
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 life. If I am not totally w
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 densit
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 beh
7 matches
Mail list logo
