[gmx-users] Re: genconf

[Vitaly V. Chaban]

Payman,

What system fo you try to simulate? How was the initial configuration
generated? Did you do EM of the small box before using genconf?

Anyway, try to decrease the time step (several orders) and start a small
(~1000 steps) MD run. If you experience the overlaps of the particles it
should help to get a better configuration. - This is to be fast.

Vitaly

On Wed, Jul 22, 2009 at 5:18 PM, Payman Pirzadeh <ppirzade at ucalgary.ca>wrote:

>  Hi Vitaly,
>
> Problem is when I minimized the system, the potential energy will become
> sth positive of the order of 10^21 and the force experienced by an atom
> becomes infinity. This will cause the simulation to crash!
>
>
>
> Payman
>
>
>
> *From:* Vitaly V. Chaban [mailto:vvchaban at gmail.com]
> *Sent:* July 22, 2009 2:20 AM
> *To:* Payman Pirzadeh; gmx-users at gromacs.org
> *Subject:* Re: genconf
>
>
>
> 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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