Hi David,
I have checked the mdout.mdp and as you said it has pbc = xyz. What do
I do now. I havent run editconf, but why it is taking pbc conditions? How
do I remove these??
thanks
Anwar
----------------------
Mohd Anwaruddin
Project Assistant
C/o DR.H.A.Nagarajaram
Lab of Computational Biology and Bioinformatics
Center for DNA Fingerprinting and Diagnostics(CDFD)
Nacharam
Hyderabad-500 076
INDIA.
Tel: +91-8413-235467,68,69,70 ext 2019
[EMAIL PROTECTED]
-----------------------
---------REPLY TO-------------
Date:Thu Sep 07 18:00:08 GMT+08:00 2006
FROM: [EMAIL PROTECTED]
To: gmx-users@gromacs.org
Subject: gmx-users Digest, Vol 29, Issue 14
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Today's Topics:
1. Re: invacuo minimization (David van der Spoel)
2. LIE energy calculation! (Mikko Hellgren)
----------------------------------------------------------------------
Message: 1
Date: Thu, 07 Sep 2006 10:44:52 +0200
From: David van der Spoel <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] invacuo minimization
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
[EMAIL PROTECTED] wrote:
> Dear gmx users,
> When I am minimizing a trimer protein in vacuum by SD as well as CG methods,
> one of the monomer gets apart from the rest of the protein and places
itself
> away from the other two monomers, which are intact. No periodic box is
> assigned. But when I am running editconf and assigning a box, then the
> structures are intact. What is the reason for the above behaviour?
> I am pasting the em.mdp below:
chekc your mdout.dmp, the default pbc = xyz
>
> cpp = /lib/cpp
> define = -DFLEX_SPC
> constraints = none
> ;integrator = CG
> integrator = steep
> nsteps = 1000
> ;
> ; Energy minimizing stuff
> ;
> emtol = 100
> ;for SD
> emstep = 0.1
> ;for CG
> ;emstep = 0.001
>
> nstcomm = 1
> ns_type = grid
> rlist = 1
> rcoulomb = 1.0
> rvdw = 1.0
> Tcoupl = no
> Pcoupl = no
> gen_vel = no
>
>
> Anwar
>
> ----------------------
> Mohd Anwaruddin
> Project Assistant
> C/o DR.H.A.Nagarajaram
> Lab of Computational Biology and Bioinformatics
> Center for DNA Fingerprinting and Diagnostics(CDFD)
> Nacharam
> Hyderabad-500 076
> INDIA.
> Tel: +91-8413-235467,68,69,70 ext 2019
> [EMAIL PROTECTED]
> -----------------------
>
>
>
> -
>
> _______________________________________________
> gmx-users mailing list gmx-users@gromacs.org
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--
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596, 75124 Uppsala, Sweden
phone: 46 18 471 4205 fax: 46 18 511 755
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
Message: 2
Date: Thu, 07 Sep 2006 11:31:39 +0200
From: Mikko Hellgren <[EMAIL PROTECTED]>
Subject: [gmx-users] LIE energy calculation!
To: "gmx-users@gromacs.org" <gmx-users@gromacs.org>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="us-ascii"
Hi Dear users, I have started to do calculations of the binding between
a protein and different ligands. I have read articles on the LIE method
and one tutorial. But still I have some quite general questions. I am
using Cut-off and NVT ensamble.
1. When I run my ligands in a water solution without the protein, should
I add counterions (Cl and Na) at physiological concentrations (about
10mM to 100mM) or make the system neutral with one or two ions or can I
ignore any ions the simulation.
2. Should I put any restraints on the ligand in the simulation without
the protein?
3. When I run my ligand bound to the protein. Should I put restraints
(c-alpha, all atoms) on both protein and ligand or only protein or
ligand or neither of them? My initial thought would be to put restraint
on c-alpha of the protein and let the rest of the system be "free".
Mikko
____________________________________________________
One cannot avoid making mistakes if one tries to produce a set of words,
or of mathematical formulae, to describe nature. Nature is more
complicated than language or mathematics. Nevertheless, one must do
one's best to produce a set of symbols which are not to discordant with
the facts.
J.B.S. Haldane, preface to "What is Life?", Lindsay Drummond, 1949
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