[gmx-users] Re: WCA and free energy calculations

2007-06-24 Thread David Mobley
Hi, I'm CCing the users list on this since it might be of general interest. I can't begin to tell you already how much help you've given me with your gromacs user-list posts and free energy tutorial. Glad I can help! I was searching the Gromacs user list and came across a thread by you tit

Re: [gmx-users] superimpose pdbs

2007-06-24 Thread Yang Ye
Pymol http://pldserver1.biochem.queensu.ca/~rlc/work/teaching/BCHM823/pymol/alignment/ It has a bit ease of use than g_confrm that it offers more richer choices for selecting atoms to be matched. See what fits to your needs. Regards, Yang Ye On 6/25/2007 1:10 AM, Alan wrote: Hi! It may be a

Re: [gmx-users] Energy minimization problem with Double precision and mpi

2007-06-24 Thread David van der Spoel
Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Sunday, June 24, 2007 4:18 AM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah

RE: [gmx-users] Energy minimization problem with Double precision and mpi

2007-06-24 Thread Josiah Zayner
> -Original Message- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > On Behalf Of David van der Spoel > Sent: Sunday, June 24, 2007 4:18 AM > To: Discussion list for GROMACS users > Subject: Re: [gmx-users] Energy minimization problem with Double precision > andmpi > > Josiah Zayne

RES: [gmx-users] superimpose pdbs

2007-06-24 Thread Caio Julio Martins Veloso
Hi Alan, You may use TOPOFIT. Caio. -Mensagem original- De: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] nome de Alan Enviada em: domingo, 24 de junho de 2007 14:11 Para: Gromacs Assunto: [gmx-users] superimpose pdbs Hi! It may be a bit GMX off-topic: I am looking for a

[gmx-users] Regarding minimization of POPE:POPG lipid bilayer

2007-06-24 Thread chris . neale
I built a POPE:POPG bilayer in 3:1 ratio. Simplify. Start with pure POPE and pure POPG first. When I am minimizing the bilayer, bonds in head groups are breaking in POPE and POPG lipid molecules. Your topologies are incorrect. Start with a simple test system: a single POPE in vaccuum. w

Re: [gmx-users] superimpose pdbs

2007-06-24 Thread David van der Spoel
Alan wrote: Hi! It may be a bit GMX off-topic: I am looking for a command line superimpose application that would be able to get all individual pdb files in folder and generated new pdb versions of them 3D superimposed. g_confrms Something like what SuperPose (http://wishart.biology.ualbe

[gmx-users] superimpose pdbs

2007-06-24 Thread Alan
Hi! It may be a bit GMX off-topic: I am looking for a command line superimpose application that would be able to get all individual pdb files in folder and generated new pdb versions of them 3D superimposed. Something like what SuperPose ( http://wishart.biology.ualberta.ca/SuperPose/help.html) d

Re: [gmx-users] Energy minimization problem with Double precision and mpi

2007-06-24 Thread David van der Spoel
Josiah Zayner wrote: -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of David van der Spoel Sent: Saturday, June 23, 2007 4:36 PM To: Discussion list for GROMACS users Subject: Re: [gmx-users] Energy minimization problem with Double precision andmpi Josiah

Re: [gmx-users] editconf -translate help

2007-06-24 Thread David van der Spoel
Shayla Fitzsimmons wrote: I have a box which contains a slab of carbon (solid) that is centered within the box. However, I want the slab to be at the very right side of the box - I know I must use editconf -translate to do this, however I cannot seem to make it work. The slab is centered has th