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 <ppirz...@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-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,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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