Re: [gmx-users] uneven distribution of water across the bilayer

Dear Mark, Thanks a lot for your valuable time, and sorry for inappropriate description, I am describing again, I hope thin time I can make it clear. I took preequilibrated POPE.pdb files which already have SPC water molecules I had deleted these water molecules and change the box size at 'Z

[gmx-users] Pull code with runtype start

Hello everyone, I just want to clarify if the runtype start option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. If I have runtype = start in my pull.ppa file then gromacs gives me an error:

Re: [gmx-users] Pull code with runtype start

dtmirij wrote: Hello everyone, I just want to clarify if the runtype start option works in gromacs-3.3.1. I didn't see anything in the mailings list suggesting that it doesn't. Did you try searching the manual for runtype? Mark ___ gmx-users

Re: [gmx-users] applying force and fixing atoms in gromacs

Ah, groovy, I was clearly using the wrong search terms, and didn't make the connection when I was looking through the contents. Cheers -Adam On 10/19/07, Mark Abraham [EMAIL PROTECTED] wrote: Adam Fraser wrote: Hello, I was looking in the manual for how to fix atoms and apply constant

RE: [gmx-users] qasi-harmonic entropy calculation

Hi Pedro, I am using 4565.9 as a conversion factor. I dont see any problem unless any condtion I needed to satisfy during the simulation. Simulation gave the result what I had expected. With regards, Abu Naser School Of Life Sciences Heriot-Watt University Edinburgh EH14 4AS Email:

Re: [gmx-users] uneven distribution of water across the bilayer

Alok wrote: Dear All, I am trying to simulate lipid-water system (340 POPE lipids 6120 TIP4P Waters), during the solvation by genbox, It also add the the water at the interior of the bilayer. I removed those water molecules by my perl script. But after removing these water molecules I have

[gmx-users] uneven distribution of water across the bilayer

Dear All, I am trying to simulate lipid-water system (340 POPE lipids 6120 TIP4P Waters), during the solvation by genbox, It also add the the water at the interior of the bilayer. I removed those water molecules by my perl script. But after removing these water molecules I have observed a

[gmx-users] applying force and fixing atoms in gromacs

Hello, I was looking in the manual for how to fix atoms and apply constant (or time dependent) force to atoms. Could someone please help me get started with this? Thank you, Adam ___ gmx-users mailing listgmx-users@gromacs.org

RE: [gmx-users] 1-4 table size of 0 nm

From: Adrien Leygue [EMAIL PROTECTED] Reply-To: Discussion list for GROMACS users gmx-users@gromacs.org To: Discussion list for GROMACS users gmx-users@gromacs.org Subject: [gmx-users] 1-4 table size of 0 nm Date: Fri, 19 Oct 2007 14:47:27 +0300 Dear Gromacs users, I am using Gromacs with a