[gmx-users] genconf

Payman Pirzadeh ppirzade at ucalgary.ca
Wed Jul 22 02:04:35 CEST 2009

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?




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


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 
!!! Looking for a postdoctoral position !!!

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