[gmx-users] au--protein separate equilibration

2013-01-17 Thread fatemeh ramezani
1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: title   =  n.pdb cpp =  /lib/cpp define  =  -DFLEXIBLE constraints =  none integrator  =  steep dt  

Re: [gmx-users] au--protein separate equilibration

2013-01-17 Thread Justin Lemkul
On 1/17/13 12:15 PM, fatemeh ramezani wrote: 1. For separate equilibration of AU and Protein, I'm using this em.mdp file for equilibration in step 1, that Protein and SOL are frozen: This is not an equilibration, this is an energy minimization, which will likely not accomplish much with so

Fw: [gmx-users] au--protein separate equilibration

2013-01-17 Thread fatemeh ramezani
Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . By these em.mdp files if I freeze only protein for the first time and after minimization I use the result .pdb file for second step of minimization that I freeze AU atoms in it,

Re: [gmx-users] au--protein separate equilibration

2013-01-17 Thread Justin Lemkul
On 1/17/13 2:48 PM, fatemeh ramezani wrote: Dear Justin thanks for your reply and, Please help me to correct the settings of .mdp files step by step . I did that in my previous reply. By these em.mdp files if I freeze only protein for the first time and after minimization I use the result