[gmx-users] RMSD/Points on different curves

Junfang.Zhang at csiro.au Junfang.Zhang at csiro.au
Thu Feb 23 23:31:48 CET 2006

Thank you very much, Tsjerk.






-----Original Message-----
From: gmx-users-bounces at gromacs.org
[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Tsjerk Wassenaar
Sent: Thursday, 23 February 2006 5:39 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] RMSD/Points on different curves


Hi Junfang,

It is not a problem that your molecule seems to be hanging out of the
box. Remember that the actual simulation system is infinitely stacked
and that that greater part of your molecule is simultaneously hanging
from a neighbouring box in your central one :)

The jumps in RMSD can only be explained (at first glance) if you have a
multimer. In that case, if one part jumps, the RMSD will jump too.
Running trjconv with the option "-pbc nojump" can solve this.



On 2/23/06, Junfang.Zhang at csiro.au <Junfang.Zhang at csiro.au> wrote: 

Dear Gromacs users,

GROMACS prefers to keep a whole molecule connected and uses the first 
atom/protein group in the molecule as a reference position.

I used PBC in the simulation, but I found the large part of one polymer
chain is out of the simulation box. Is that a problem?

When I analyzed the RMSD, the points lay on three different curves, the 
lowest one goes to zero for zero time. The other two curves lie some
constant distance above it. It is most likely related to periodic
boundary conditions.

Can you please let me know how to solve these problems? 

Thank you in advance,

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Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336

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