[EMAIL PROTECTED] wrote:
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??
pbc=no

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]
-----------------------



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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
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