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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