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
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
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,
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
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