[gmx-users] solvent box

Stud_Psychopharm stu_psyc at nimhans.kar.nic.in
Thu Feb 12 07:46:01 CET 2004

sadhna, you can try with this command
editconf -f input.gro -d 0.8 -c -o output.gro

hope you might not given -c command in your job..  I had the same 
problem, it worked out after giving "-c" at editconf command..
all the best
"The more we learn the more we realize how little we know." - 
R.Buckminster Fuller 

Blaise M.
Graduate Student,
Department of Psychopharmacology,
National Institute of Mental Health And Neuro Sciences (NIMHANS),
India. Tel: 91 80 6995112.

-----Original Message-----
From: sadhna <sadhana at che.iitb.ac.in>
To: <gmx-users at gromacs.org>
Date: Thu, 12 Feb 2004 11:50:21 -0500 (GMT)
Subject: [gmx-users] solvent box

> hi all,
>        While doing MD in water my peptide is not confined to the centre
> of the box and sometimes a part of the peptide also goes out of the
> box,
> though i have used box size of appropriate length. where could be the
> problem?
> thanks in advance
> sadhna
> Sadhna Joshi
> Research Scholar
> Dept of Chemical Engg
> Indian Institute of Technology,Powai
> Mumbai-400076
> India
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