Payman Pirzadeh wrote:
Hi Justin,
I checked the trjconv help. It also takes .gro files. If so, do I still need
to provide a .tpr file? (if yes, then the output can be .gro?)
Any of the listed file formats can be input or output. To fix "broken"
molecules, you must supply a .tpr file. If you run trjconv without it, you will
get an error.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 22, 2009 6:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
Hello,
I minimized the initial output (from another simulation) first; then I
replicated it. This time, the minimization of the bigger box was done more
easily! I ran an MD simulation with the bigger box and after 6 hours, it
has
not crashed yet.
But, I have a question. When we replicate a box, and in the primary box
one
molecule is dissected into pieces due to pbc, will GROMACS return the
molecules to its original shape during MD run or not?
No, it does not.
I believe, without minimization, these dissected pieces will remain in the
middle of the box and interfere with their replicated versions. Maybe,
'genconf' should be modified for such replications to maintain the pbc
between the new molecules at the boundaries and fix the problem with the
particle in the middle of the new bigger box!
It can easily be accomplished using a .tpr file, and by using trjconv -pbc
whole. After molecules are whole, then use genconf.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 22, 2009 9:22 AM
To: 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] genconf
Thanks a lot Mark! I will run the system for equilibration and then try to
replicate it. I will keep you guys posted.
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Mark Abraham
Sent: July 21, 2009 11:01 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
Yes and no!
Sometimes there is an overlap, but sometimes I could find nothing! In the
simplest case, how can we avoid overlaps in a way that the crystal
structure
is maintained under pbc?
Can the option "-dist" help here?
Replicating a box that was not designed for periodicity will always have
this problem. Whether the box is too small or two large, there will
either be steric clashes, or vacuums that will need filling. The general
solution is to equilibrate your box under PBC prior to replication. Now
the box size and the atomic spacings will be plausible, and the
replication will not of necessity introduce artifacts.
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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