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?
Maybe. I've never had to use it. I've replicated a few systems using genconf
-nbox (water and lipids), but I've never encountered any problems. In theory,
PBC should be maintained since all genconf is doing is translating your system
by a certain factor according to box dimensions.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:47 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
I am so sorry! I had sth in mind and I wrote sth else!!!
My original box has zero charges and GROMACS shows no notes on this.
As soon as the box is multiplies, then the note regarding the net charge
shows up and causes the simulation to crash.
Well, then, like I said, this is probably an accumulation of rounding
errors.
It can probably be ignored. The reason for the crash is more likely some
kind
of atomic overlap generated by the use of genconf.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:25 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
In my previous e-mail, I posted the amount of charge given by GROMACS:
NOTE 2 [file sixsitemodel.top, line 8]:
System has non-zero total charge: -1.220703e-04
Also, I run the system without multiplication, and it runs fine without
any
notes on the presence of a net charge!!! But, as soon as it is
multiplied,
then it gives notes of net charge!
Then I'm more confused (and hence why I asked the first time). You said
your
original system had a non-zero charge. Now you say that there were no
notes
about net charge, so the original system was uncharged.
Depending on the size of your system, small rounding errors can accumulate
and
cause tiny fractional charges. I don't know if this is problematic or not
(in
terms of the system charge that mdrun finds), but it could be why you are
seeing
this note.
-Justin
Payman
-----Original Message-----
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org]
On Behalf Of Justin A. Lemkul
Sent: July 21, 2009 6:13 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genconf
Payman Pirzadeh wrote:
OK! Thanks for the tips on thermostat.
I multiplied my .gro file by using the command "genconf". My original
box has non-zero charge, but the generated bigger box has some charges:
Define "non-zero." Is it at least an integer? Should your system bet
net
neutral at this stage in your system preparation?
-Justin
NOTE 2 [file sixsitemodel.top, line 8]:
System has non-zero total charge: -1.220703e-04
Then, during minimization, the system experiences a large positive
potential and infinite force. Is there a technicality in using "genconf"
that I am missing? Doesn't it read the dimensions of the box from .gro
file to make sure no particles are overlapping with the original box? Or
no particle is coming from the new one in the old one?
Payman
*From:* gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Vitaly V. Chaban
*Sent:* July 21, 2009 4:53 PM
*To:* gmx-users@gromacs.org
*Subject:* [gmx-users] Re: reliability of NOTES
Hello,
I am trying to prepare the input files for an MD run. After running
grompp,
I received the following note:
NOTE 1 [file npt.mdp, line unknown]:
The Berendsen thermostat does not generate the correct kinetic
energy
distribution. You might want to consider using the V-rescale
thermostat.
How reliable this note is?
It's true.
And how can I implement V-rescale thermostat in y
input file (I found nothing in the manual).
Substitute "berendsen" with "V-rescale" in the mdp file.
Also, when I changed the thermostat to nose-hoover, it said that it
can not
be used with Berendsen barostat. Why?
C'est la vie...
--
Vitaly V. Chaban, Ph.D. (ABD)
School of Chemistry
V.N. Karazin Kharkiv National University
Svoboda sq.,4, Kharkiv 61077, Ukraine
email: cha...@univer.kharkov.ua
<mailto:cha...@univer.kharkov.ua>,vvcha...@gmail.com
<mailto:vvcha...@gmail.com>
skype: vvchaban, mob.: +38-097-8259698
http://www-rmn.univer.kharkov.ua/chaban.html
===================================
!!! Looking for a postdoctoral position !!!
===================================
------------------------------------------------------------------------
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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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