Re: [gmx-users] protein membrane system

2012-12-25 Thread Justin Lemkul
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

2012-12-25 Thread Shima Arasteh
: 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

Re: [gmx-users] protein membrane system

2012-12-25 Thread Justin Lemkul
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

[gmx-users] protein membrane system

2012-12-24 Thread Shima Arasteh
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

[gmx-users] protein membrane system

2012-12-24 Thread Shima Arasteh
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

Re: [gmx-users] Protein-membrane system

2011-02-17 Thread Justin A. Lemkul
*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

Re: [gmx-users] Protein-membrane system

2011-02-16 Thread Justin A. Lemkul
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

Re: [gmx-users] Protein-membrane system

2011-02-16 Thread Itamar Kass
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

Re: [gmx-users] Protein-membrane system

2011-02-16 Thread Jianguo Li
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