Your system will explode.
Actually I'm not sure, why that is, but probably, because some forces
from the bonded terms are transferred to your mass-zero particle, which
then accelerates infinitly fast...even though I would expect some
division over zero error in the velocity calculation...
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Wang Qin wrote:
Thank you, Maik.
I do want to do standard FEP and thank you for telling me that FEP don't
go with virtual sites. It does help.
BTW, may I ask you why I should define a none_zero mass for a dummy atom?
Thanks,
Qin
On 8/8/07, *Maik Goette* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Friend...
What are you trying to do???
If you want to do standard FEP with growing something into dummy (NOT
virtual site) or from dummy, you must not use virtual sites!
Virtual sites in fact, have no mass; neither in A- nor in B-state.
Please read the fManual about virtual particles, their usage and why
they exist in GROMACS (hint, delocalized charge)....
As far as I know, you can't morph a virtual site to a real particle. I
also think, It wouldn't make much sense, though.
If you want to morph away e.g. a proton, define a dummy in the b-state,
which has no LJ parameters (eps and sigma=0) and no charge, but still
the original mass.
Regards
Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel. : ++49 551 201 2310
Fax : ++49 551 201 2302
Email : mgoette[at]mpi- bpc.mpg.de <http://bpc.mpg.de>
mgoette2[at]gwdg.de
WWW : http://www.mpibpc.gwdg.de/groups/grubmueller/
Wang Qin wrote:
> Hi,
> Thanks for reply. It seems that specifying mass_B = mass_A doesn't
> help to solve the problem. However, if I don't use the directory
> [virtual_site#] the errors disappear! What's the result if I do
this?
> Is the directory necessary in the FEP calculation to define
the dummy
> atoms?
> Thanks,
> Qin
>
> On 7/20/07, *Stéphane Téletchéa* < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
> <mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>>> wrote:
>
> Wang Qin a écrit :
> > Hi there,
> > I have a problems when I do a FEP calculation.
> > Below is how I defined dummy atoms in the topology
file:
> > [atom]
> > ;nr type resnr residue atom cgnr charge
> > mass type_B charge_B mass_B
> > 21 opls_172 1 LG6 H21 21 0.4650
> > 1.00800 opls_0 0.0000 0.000000
> > 22 opls_172 1 LG6 H22 22 0.4650
> > 1.00800 opls_0 0.0000 0.000000
> > ......
> >
>
> I think you need to specify the mass_B=mass_A, at least this
is how it
> is setup in the tutorials i've done (the one from Berk Hess
and the
> other one from David Mobley).
>
> I've also done calculations without setting the mass for B
(like you
> did) and did not encounter any problem, the error you're
seing could
> thus come from another part of your system.
>
> Cheers,
> Stéphane
>
> --
> Stéphane Téletchéa, PhD. http://www.steletch.org
> Unité Mathématique Informatique et Génome
http://migale.jouy.inra.fr/mig
> INRA, Domaine de Vilvert Tél : (33) 134 652 891
> 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901
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