[gmx-users] fail to pull

Albert mailmd2011 at gmail.com
Sun Apr 7 18:05:05 CEST 2013

hello Justine:

  thanks a lot for such kind comments.

  I may find the problem, the COM probably is not suitable to use whole 
protein since I found by g_dist that all the distance are between 
0.9-1.0 nm throughout the whole pulling process.

  BTW, I notice that we are using command:

grompp -f md_pull.mdp -c npt.gro -p topol.top -n index.ndx -t npt.cpt -o pull.tpr

for pulling .tpr generating. May I ask whey shall we use option

"-t npt.cpt"

in  this  step? Usually we only need to specify .mdp, .gro and .top file 
for .tpr file....

thank you very much

On 04/07/2013 05:31 PM, Justin Lemkul wrote:
> Let me clear one thing up first. 1 ns of pulling with a 0.001 nm/ps pull
> rate will not necessarily cause the ligand to be displaced by 1 nm. The
> particle pulling the virtual spring will be displaced by 1 nm, but the
> ligand will only move as a function of this applied force and the restoring
> forces (i.e. interactions between the ligand and protein).
> Choosing a more suitable reference group and running the simulation for
> longer will produce the desired result.
> -Justin

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