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-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 !!! > =================================== > > > ------------------------------------------------------------------------ > > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- ======================================== 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 ======================================== _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
