[gmx-users] Re: genconf

[Vitaly V. Chaban]

Payman,

Such little charge cannot produce large energies, so it seems you should run
EM first and everything will be OK with your simulation.

As far as understand non-zero charge is a resuts of averaging errors (during
grompp!), you cannot remove this warning.

~ Vitaly

On Wed, Jul 22, 2009 at 3:04 AM, Payman Pirzadeh <ppirzade at ucalgary.ca>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:
>
>
>
> 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,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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