I am so sorry! I had sth in mind and I wrote sth else!!! My original box has zero charges and GROMACS shows no notes on this. As soon as the box is multiplies, then the note regarding the net charge shows up and causes the simulation to crash.
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 6:25 PM To: Gromacs Users' List Subject: Re: [gmx-users] genconf Payman Pirzadeh wrote: > 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! > Then I'm more confused (and hence why I asked the first time). You said your original system had a non-zero charge. Now you say that there were no notes about net charge, so the original system was uncharged. Depending on the size of your system, small rounding errors can accumulate and cause tiny fractional charges. I don't know if this is problematic or not (in terms of the system charge that mdrun finds), but it could be why you are seeing this note. -Justin > 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? 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