[gmx-users] genconf

[Payman Pirzadeh]

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!

Payman







-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at 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-bounces at gromacs.org 
> [mailto:gmx-users-bounces at gromacs.org] *On Behalf Of *Vitaly V. Chaban
> *Sent:* July 21, 2009 4:53 PM
> *To:* gmx-users at 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: chaban at univer.kharkov.ua 
> <mailto:chaban at univer.kharkov.ua>,vvchaban at gmail.com 
> <mailto:vvchaban at 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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