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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