Payman Pirzadeh wrote:
You were right! The dimensions of the box are zero in the .gro file. Should
I change them to the values I have?
As long as those vectors define the box size and not necessarily the system size
(i.e., largest coordinate - smallest coordinate). You can do this with a .pdb
file, I think on the CRYST line, if you prefer.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 12:08 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
But, I am using a .pdb file as the input of the gromacs. Does the
preparation of pdb file differ from software to software?
It shouldn't, and I'm not 100% sure on how Gromacs handles system size from
a
.pdb file (I always use .gro). What you can try to do is transform your
.pdb
into .gro format with editconf, and read the last line of the .gro file.
That's
any easy way to determine the size of the box Gromacs is finding.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 16, 2009 11:42 AM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
Previously, my box was 27.154*31.354*103.386 (all in A) and I reduced the
rvdw cutoff to 10A, but problem was still there.
Now I made my box bigger by using a visualization software. The new
dimensions are ~54*63*103.38(all in A). Again the same warning is given
to
me about increasing the box size or reduce the rvdw.
Well, Gromacs doesn't do anything in A, it's all nm, so be sure that
everything
you're doing is consistent with Gromacs conventions. There is no reason
that
either of those boxe should be complaining about a 1.0-nm cutoff, so there
has
to be something that messed up along the way.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 15, 2009 7:32 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
I have an .pdb file from another simulation. I want to make the
appropriate
input files to run a simulations. I have used grompp to produce the .tpr
file, but I get the usual ERROR:
ERROR: The cut-off length is longer than half the shortest box vector
or
longer than the smallest box diagonal element. Increase the box size or
decrease rvdw.
I decreased the rvdw to 1.0 nm, (my rlist and rcoulumb are 0.9) but
still
the problem persists! Smaller rvdw is not good for my system. Any
suggestions?
Then you'll have to use a bigger box, most likely. What is your smallest
box
vector? That should indicate the limits of your cutoffs.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of David van der Spoel
Sent: July 15, 2009 12:23 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Thanks Justin.
Unfortunately, I realized that after I sent the e-mail. Anyways, I
started
running to models: SPCE and TIP4P to check the energies of these
systems
to
figure out where the problem with my own system (six-site model) could
be.
I
will keep you posted. But, I have a question about the compressibility
factor used in .mdp file. Does that(if it is not a correct value) truly
affect the simulation when the reference pressure is set?
No, only the relaxation rate (with Berendsen scaling) resp. the
oscillation period with Parrinello Rahman.
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 15, 2009 11:38 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hi again,
I have a question about the .itp files. When e.g. TIP4P.itp the
atomtypes
in
the [atoms ]are specifies as opls_???, doesn't grompp check the
database
for the corresponding parameters? Or we should again manually specify
the
[
atomtypes ] again in either .itp or .top file?
You need to #include "ffoplsaa.itp" to take care of everything related
to
the
OPLS-AA force field. Invoking grompp is not magic, the topology has to
contain
specific instructions for everything you need to handle in your system.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Payman Pirzadeh
Sent: July 15, 2009 10:14 AM
To: jalem...@vt.edu; 'Discussion list for GROMACS users'
Subject: RE: [gmx-users] making a box of water
OK!
I changed my .top file to
;This is simulation for TIP4P water model
[ defaults ]
; non-bondedtype combrule genpairs FudgeLJ
FudgeQQ N
1 2 NO
; include TIP4P topology
#include "tip4p.itp"
[ system ]
Pure box of water
[ molecules ]
SOL 506
But I still get the same error message! Should I include the
[defaults]
in
the .itp file?
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 7:56 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Will #include "ffgmx.itp" solve my problem? Would it be a general
solution
or in each case I should specify (if I add other solutes such as
proteins)?
Well, ffgmx is deprecated, so it is probably not the best choice :)
Choosing a
force field should not be a haphazard occasion, it is a very important
choice.
For water models, parameters should be uniform, but if you're
simulating
a
protein, you'll want to make a very educated decision.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 7:07 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] making a box of water
You need to #include an appropriate force field that contains the
[defaults],
[atomtypes], etc. before you can define a [moleculetype].
-Justin
Payman Pirzadeh wrote:
Here is my .top file:
;This includes SPC-E potential
#include "spce.itp"
[ system ]
Pure box of water
[ molecules ]
SOL 515
I used the same thing with my own model, but it had worked.
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 14, 2009 6:54 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] making a box of water
Payman Pirzadeh wrote:
Hello,
I am trying to make a box of water from three different water
models.
I
can make one from my own water model, but when I want to test TIP4P
and
SPCE, as soon as it comes to energy minimization step and using
grompp,
I get the following error message:
Program grompp, VERSION 4.0.4
Source code file: topio.c, line: 415
Fatal error:
Syntax error - File spce.itp, line 1
Last line read:
'[ moleculetype ]'
Invalid order for directive moleculetype
What is the problem causing the code referring to itp file?
See the message I just sent. Something is out of order in your .top
file.
-Justin
Regards,
Payman
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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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