[gmx-users] problem with g_density -center

Sorry, Ali, it's not really possible for me to simplify those commands. That's about as simple as it gets. I suggest that you start a normal post that follows the form: I did this (paste commands) and I got this (paste error message). Also, when you get a message like Fatal error: Invalid

[gmx-users] problem with g_density -center

Dear Ali: Please also keep in mind that 99% of the papers published with gromacs using NpT have shown density profiles along Z that were computed simply by using (the incorrect) trjconv -center and (the incorrect for NpT) g_density. So while I think that it's always important to get things

[gmx-users] problem with g_density -center

My point is that the old paper probably used the incorrect trjconv/g_density as well so to reproduce it you may be best off using the standard gromacs. Chris. -- original message -- Thank you so much for your reply but it is very important for me that i can reproduce results of a paper or

[gmx-users] problem with g_density -center

Sorry Ali, I can't do your work for you. If this is way over your head, then either forget it, find a colleague to help you, or spend some time learning bash and gromacs. I'n not commenting on your approach, but if you modified your .gro then you need a new .top file. You can create one.

[gmx-users] problem with g_density -center

out exactly what methods they used and use those same methods. Chris. -- original message -- Ali Alizadeh ali.alizadehmojarad at gmail.com Fri Oct 19 20:22:54 CEST 2012 Previous message: [gmx-users] problem with g_density -center Messages sorted by: [ date ] [ thread ] [ subject ] [ author

[gmx-users] problem with g_density -center

Hi,   I am trying to calculate the density profile of  head group of bilayer normal to z direction using gromacs 4.0.7. I was trying to center the density profile about dx/2.dy/2,0 . But, I am finding problem with using center option. I find using -center option does not shift the bilayer to

Re: [gmx-users] problem with g_density -center

Sanku M wrote: Hi, I am trying to calculate the density profile of head group of bilayer normal to z direction using gromacs 4.0.7. I was trying to center the density profile about dx/2.dy/2,0 . But, I am finding problem with using center option. I find using -center option does not

[gmx-users] problem with g_density -center

g_density is not compatible with constant pressure simulations. You must modify it to construct the bins outward from the bilayer center when doing NPT: http://lists.gromacs.org/pipermail/gmx-users/2010-November/055651.html Further, trjconv -center is misleading. I actually lost a lot of

Re: [gmx-users] problem with g_density -center

Dear Email Sender, Thank you very much for contacting me! Unfortunately, I am not available in the office at the moment and cannot respond to your email. I will be able to handle your request starting again Monday, August 22, 2011. For all questions about CloudBroker and the CloudBroker