> > wouldn't worry about this.
> > > > The chance that the last water block is willingly smaller than the
> > > > number of ions is about zero.
> > > >
> > > > Berk
> > > >
> > > > > Date: Thu, 11 Feb 2010 13:34:
o see the difference between
crystal water and normal water.
Berk
> Date: Thu, 11 Feb 2010 13:07:41 +
> From: t.pig...@bristol.ac.uk
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
>
> Plus I suppose that if yo
Hi,
Yes, but genion is not smart enough (yet) to see the difference between crystal
water and normal water.
Berk
> Date: Thu, 11 Feb 2010 13:07:41 +
> From: t.pig...@bristol.ac.uk
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not
water block is willingly smaller than the
number of ions is about zero.
Berk
> Date: Thu, 11 Feb 2010 13:34:59 +0100
> From: er...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
>
> Hi,
>
> Is
t; From: er...@xray.bmc.uu.se
> To: gmx-users@gromacs.org
> Subject: Re: [gmx-users] Software inconsistency error: Not enough water
>
> Hi,
>
> Is it desirable that genion only considers a single SOL block? Why not
> use them all if there are many?
>
> Regards,
>
> Erik
From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 16:45:06 +0530
Subject: Re: [gmx-users] Software inconsistency error: Not enough water
To: gmx-users@gromacs.org
Thanks berk.
By the way, if I dont give -p topol.top as input to genion
Hi,
genion in future Gromacs versions will only use the last SOL block
and give a proper error message when there is not enough water.
Berk
From: iitd...@gmail.com
Date: Thu, 11 Feb 2010 16:45:06 +0530
Subject: Re: [gmx-users] Software inconsistency error: Not enough water
To: gmx-users
you provided does not have enough SOL molecules in the [molecules ]
> section.
> I'll fix this error message for the next release.
>
> Berk
>
> --
> From: iitd...@gmail.com
> Date: Thu, 11 Feb 2010 12:48:53 +0530
> To: gmx-users@gromacs
the first SOL entry.
Berk
From: g...@hotmail.com
To: gmx-users@gromacs.org
Subject: RE: [gmx-users] Software inconsistency error: Not enough water
Date: Thu, 11 Feb 2010 11:08:38 +0100
Hi,
This error message in incorrect, it is probably not a software inconsistency.
Looking at the code, it
iitd...@gmail.com
Date: Thu, 11 Feb 2010 12:48:53 +0530
To: gmx-users@gromacs.org
Subject: [gmx-users] Software inconsistency error: Not enough water
Hello gmxusers !!
I am simulating a protein and it is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP simulation too
Hello gmxusers !!
I am simulating a protein and it is bound to ATP.
Simulation of protein alone (without) works fine. Solely ATP simulation too
works. But the problem arises on adding ions to the protein + ATP (1QHH.pdb)
file.
Error:
$ genion -s em.tpr -o ion.pdb -p topol.top -np 48
WARNING: tur
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