[gmx-users] Regarding Minimization

2011-11-04 Thread Ravi Kumar Venkatraman
*Dear all,** * *I wanted to minimize the energy of a single molecule. How emtol and emsteps I have to put to get optimised single molecule structure.* * * *Thank you** * * * *With Regards, Ravi Kumar Venkatraman, IPC Dept., IISc, Bangalore, INDIA. +91-9686933963.* -- gmx-users

Re: [gmx-users] Regarding Minimization

2011-11-04 Thread Mark Abraham
On 4/11/2011 5:14 PM, Ravi Kumar Venkatraman wrote: *Dear all,** * *I wanted to minimize the energy of a single molecule. How emtol and emsteps I have to put to get optimised single molecule structure.* * Set them to whatever size seems reasonable to you and leaves you with 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.

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

2007-06-23 Thread naga raju
Dear gmx users, I downloaded POPE.itp and lipid.itp files from Dr.Tieleman website http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies and POPG.itp file from Dr.Mikko Karttunen wesite http://www.apmaths.uwo.ca/~mkarttu/downloads.shtml. I built a