try to set the value of emtol to about 10000 times smaller !
On Jun 20, 2009, at 4:30 PM, Ms. Aswathy S wrote:
But i am in a situation like the minimization doesn't make any
change in the energy and it convergeing at 15 th step each time. So
further minimization is not possible. Can you plz check the em.mdp
file and tell me whetehr I have given any wrong parameter?
Dept. Biotechnology
Ext. 3108
----- Original Message -----
From: "XAvier Periole" <x.peri...@rug.nl>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Saturday, June 20, 2009 7:16:26 PM GMT +05:30 Chennai,
Kolkata, Mumbai, New Delhi
Subject: Re: [gmx-users] Coordinates change after minimization
On Jun 20, 2009, at 15:30, "Ms. Aswathy S" <aswat...@amritapuri.amrita.edu
wrote:
using the g_confrm command the RMSD of the protein is 0 (Root mean
square deviation after lsq fit = 4.14581e-08). It means the
structure doesn't have a major change ultimately.. Please correct me
if I am wrong..
You are correct.
Can I move ahead with this minimization?
However this value is really small, which suggests that the
minimization did actually about nothing. This a bit too nothing!
Of I were you I would check that you actually used g_confrm the right
way or indeed performed a minization.
Dept. Biotechnology
Ext. 3108
----- Original Message -----
From: "David van der Spoel" <sp...@xray.bmc.uu.se>
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Sent: Saturday, June 20, 2009 6:07:20 PM GMT +05:30 Chennai,
Kolkata, Mumbai, New Delhi
Subject: Re: [gmx-users] Coordinates change after minimization
Justin A. Lemkul wrote:
Ms. Aswathy S wrote:
Hi,
After minimizing the protein -ligand complex, the co-ordinates have
changed
drastically.My idea about minimization was the coordinates will
have
minute
changes only. In this case my protein is completely transferring
to a new
co-ordinates.Is that reasonable.??
The amount of change will depend on the quality of the initial
model.
If large changes need to be made, they can be. If the entire
protein is
moving, then perhaps the box has not been prepared correctly, and
the
translation is caused by a periodic jump. Have a look at the output
(not just the coordinates) and see if you can deduce what's going
on.
Try running g_confrms to see whether they really are very different.
-Justin
Thanks, Aswathy Dept. Biotechnology Ext. 3108
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