#ZHAO LINA# wrote:
I used the same commands trying another proteins, but no problems. So it's not
the reason about the commands I used.
The problem is not whether or not your commands work for other systems, rather
the fact that they are (for some reason) not working for this particular system.
Most standard commands work just fine. The reason I asked originally was to
see exactly what your commands were to check if you were using the right files
instead of accidentally repeating the commands on the coordinate file with the
improper box vectors.
That is also (I suspect) the reason Dallas asked for you to copy and paste all
your commands.
We can't get inside your head to see what you're doing, so if you want free
help, you need to provide the information we ask for so we can quickly resolve
this. If grompp is still complaining about box vectors, you're either using the
wrong coordinate file, or you've somehow managed to mangle the coordinate file
format. Without seeing your actual commands and any other relevant details, the
best anyone can offer is "you're doing something wrong."
-Justin
It did not contain the same number of molecules after genion when I changed the box size. The pressure coupling was not on, and I did not reach this steps. The problem I had just the steps I did the energy minimization after ions (NA+ and CL-) added.
Thanks and regards,
lina
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 6:48 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths
Please copy and paste in the commands you are using, and the output.
I suspect you have made your box bigger, but it still contains the same
number of molecules and you still have pressure coupling on. So when you
start the simulation, not surprising that the box compresses again and
goes under 2nm again.
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble
a nail.
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
boun...@gromacs.org] On Behalf Of #ZHAO LINA#
Sent: Tuesday, 15 June 2010 12:04 AM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
behalf of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths
#ZHAO LINA# wrote:
_______________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org]
on behalf of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths
#ZHAO LINA# wrote:
Hi,
First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off
length.
Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in
the
editconf about the box size, actually this box is really large
enough
for the testing consideration, but still has the same problem.
Well, what are your box vectors? If they are < 2 nm, you will get
this error
because of the minimum image convention.
http://www.gromacs.org/Documentation/Terminology/Minimum_Image_Conventi
on
-Justin
system size : 4.581 2.380 2.715 (nm)
diameter : 4.889 (nm)
center : -0.012 0.003 -0.904 (nm)
box vectors : 0.000 0.000 0.000 (nm)
box angles : 0.00 0.00 0.00 (degrees)
box volume : 0.00 (nm^3)
shift : 9.678 9.664 5.461 (nm)
new center : 9.667 9.667 4.557 (nm)
new box vectors : 12.889 12.889 12.889 (nm)
new box angles : 60.00 60.00 90.00 (degrees)
new box volume :1514.05 (nm^3)
This one I set was really large, but still showed that problems.
What problems? The same error about the box lengths being shorter
than
twice
the cutoff? I don't think that's possible, given those vectors, if
you're
keeping your cutoffs at 1.0 nm.
-Justin
I do keep the cut-off. That's I do not know why. Four times had been
tried.
Thanks,
lina
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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