[gmx-users] Re: T-Coupling and COM removal
markus.miettinen at tkk.fi
Thu Feb 21 14:42:54 CET 2008
On Feb 20, 2008, at 19:36 , gmx-users-request at gromacs.org wrote:
> Message: 4
> Date: Wed, 20 Feb 2008 09:15:33 -0800
> From: "Ilya Chorny" <ichorny at gmail.com>
> Subject: [gmx-users] T-Coupling and COM removal
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> <5f5f916d0802200915y1beff759ye244b11775355553 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> HI All,
> I ran some membrane protein simulations and got some strange
> results. The
> RMSD (~.18 nm) of the protein equilibrated quite nicely but when I
> look at
> the trajectory the protein seems to be diffusing way to much over
> 20ns. The
> protein has about 1000 AA. I calculated the KE of the protein,
> lipid, and
> water and got a KE that was 1.5RT, 1.2RT, and .8RT respectively.
> My T is
> My COM removal and T-coupling is for the whole system. I am running
> Is there a problem with T-coupling and COM removal on the whole
If you have set nstcomm=1, you should not experience a drift.
For some reason, however, the center of mass of the whole simulation
can slowly drift, even if explicit removal (nstcomm = 1) has been set.
A Bugzilla has been posted, please see
for further details.
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