Re: [gmx-users] Targeted Molecular dynamics

I have implemented one approach to targeted MD for version 3.2.1 that uses soft restraints to achieve the transformation. We imagined we would make the code available (contribute it to Gromacs) after we submit the manuscript. Jay -- R. Jay Mashl University of Illinois [EMAIL PROTECTED

Re: [gmx-users] query about making a pdb file

See 'help save'. Apparently there is no menu option for saving the 'all' group. Jay On Thu, 29 Mar 2007, Jagannath Mondal wrote: Date: Thu, 29 Mar 2007 16:41:35 -0500 From: Jagannath Mondal <[EMAIL PROTECTED]> To: Jay Mashl <[EMAIL PROTECTED]>, Discussion

Re: [gmx-users] query about making a pdb file

PyMOL (http://pymol.sf.net) is one option for building the chain based on natural amino acids and subsequently performing mutations. Jay On Wed, 28 Mar 2007, Jagannath Mondal wrote: Date: Wed, 28 Mar 2007 23:54:27 -0500 From: Jagannath Mondal <[EMAIL PROTECTED]> Reply-To: Discussion list for

Re: [gmx-users] Re: gromacs and pH description!

with explicit solvent. Anyone interested? I think there is a general need for it. After having just finished some work on protonation states without the benefit of an implementation built into Gromacs, I have been thinking about how to do just that. Jay -- R. Jay Mas

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

abelled the lipids in > different leaflets as different molecule types, or > different chains, but it's a bit late now... > > --- Jay Mashl <[EMAIL PROTECTED]> wrote: > > > On Wed, 8 Nov 2006, Alan Dodd wrote: > > > Has anyone already created a way to gene

Re: [gmx-users] Creation of an index file with seperate lipid leaflets

On Wed, 8 Nov 2006, Alan Dodd wrote: > Has anyone already created a way to generate an index > file with the atoms from the two leaflets of a bilayer > listed seperately? I can't believe it hasn't already > been done, but can't find a direct description of a > solution. I'm attempting a modificat

Re: [gmx-users] Using g_energy in a noninteractive mode script

o manually enter (e.g., $STRING), then the command you need is echo "$STRING" | g_energy -f ener.edr For earlier version of Gromacs, use the number of the item instead, e.g., echo "13" | g_energy -f energ.edr Jay -- R.

Re: [gmx-users] Setting up a random system

On Sun, 9 Jul 2006, Mark Abraham wrote: Hello, I am trying to reproduce the assembly of phospholipids into a micel and so I fill a box using the genbox command. And then I solvate it using the same command. I have tried really hard to have it running but I get a segmentation fault at worst and at