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?
There's nothing there that would cause a problem. So long as nothing in
the .log file looks amiss, you can probably start equilibrating.
Mark
----- 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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