> No. My system is a single protein with charged ligand associated with it. But
> why should box size shrink ? In solvated system it does not shrink. What
> effect vacuum could possibly have on it ?
Sounds very much like you have pressure coupling on. Check your .mdp file.
Catch ya,
Dallas Wa
rs@gromacs.org
> Subject: Re: [gmx-users] Load imbalance and Y size error
>
> Berk Hess wrote:
> > Hi,
> >
> > Do not "randomly" change the fourierspacing.
> > Are you really using PME in vacuum?
> >
> > The box size can only change if you
Berk Hess wrote:
Hi,
Do not "randomly" change the fourierspacing.
Are you really using PME in vacuum?
The box size can only change if you have pressure coupling turned on,
which should, obviously, should not do in vacuum.
This suggests adding a warning about pressure coupling when the atomic
r (0.866052) is
smaller than the number of DD cells (2) times the smallest allowed cell
size(2.00)"
What possibly could be the reason ?
Regards,
Nikhil
From: nikhil damle
To: Discussion list for GROMACS users
Sent: Thu, 8 October, 2009 2:10:04 PM
Subject: Re: [gmx-users] Load imbalance
lowed cell
size(2.00)"
What possibly could be the reason ?
Regards,
Nikhil
From: nikhil damle
To: Discussion list for GROMACS users
Sent: Thu, 8 October, 2009 2:10:04 PM
Subject: Re: [gmx-users] Load imbalance and Y size error
No. My system is a sing
GROMACS users
Sent: Thu, 8 October, 2009 12:46:56 PM
Subject: Re: [gmx-users] Load imbalance and Y size error
nikhil damle wrote:
> Hi,
>
> I tried to run on single node now. Now the error is different saying
> "One of the box vectors has become shorter than twice the cut-off le
nikhil damle wrote:
Hi,
I tried to run on single node now. Now the error is different saying
"One of the box vectors has become shorter than twice the cut-off length
or box_yy-|box_zy| or box_zz has become smaller than the cut-off"
This means that my box shrinks during dynamics (this is not c
volume MD)
But when Solvent is present in the same system, this does not happen. How
should i deal with it then ?
Regards,
Nikhil
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Thu, 8 October, 2009 11:57:46 AM
Subject: Re: [gmx-users] Load imbal
nikhil damle wrote:
Hi all
I am trying to simulate a system of 3168 atoms in vacuum in PBC
box (-d=0.9 nm). Since there are no solvent molecules, i am unable to
neutralise the system using addition of ions (Hence system has +3
charge). As soon as i start the MD run after putting the
Hi all
I am trying to simulate a system of 3168 atoms in vacuum in PBC box
(-d=0.9 nm). Since there are no solvent molecules, i am unable to neutralise
the system using addition of ions (Hence system has +3 charge). As soon as i
start the MD run after putting the whole system in box, t
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