OMACS users
Subject: RE: [gmx-users] the box lengths
Well, there's ya problem :-)
That specifies the box dimensions.
Have a look at try2-water.pdb as well, then you should be able to pin
down where the issue has arisen. Appears that one of those steps have
failed to write the box dimensions.
ble
a nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> The
Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> There is none CRYST1 line in
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths
What is the contents of the CRYST1 line in the file try2-water-ions.pdb?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal
What is the contents of the CRYST1 line in the file try2-water-ions.pdb?
Catch ya,
Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3010
dallas.war...@pharm.monash.edu.au
+61 3 9903 9167
--
size or decrease rlist.
>
> ///////////////////////
>
> but if I still used the pbc=no, it will work fine at this steps.
>
> Thanks and regards,
&g
romacs.org [gmx-users-boun...@gromacs.org] on behalf
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 11:15 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths
As already mentioned by Justin, unless you copy and paste the commands
and output
ry problem begins to resemble
a nail.
> -Original Message-
> From: gmx-users-boun...@gromacs.org [mailto:gmx-users-
> boun...@gromacs.org] On Behalf Of #ZHAO LINA#
> Sent: Tuesday, 15 June 2010 12:32 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the
- Original Message -
From: #ZHAO LINA#
Date: Tuesday, June 15, 2010 12:34
Subject: RE: [gmx-users] the box lengths
To: Discussion list for GROMACS users
> I used the same commands trying another proteins, but no
> problems. So it's not the reason about the commands I use
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Dallas B. Warren [dallas.war...@pharm.monash.edu.au]
Sent: Tuesday, June 15, 2010 6:48 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths
Please copy and paste in the commands you are us
June 15, 2010 6:48 AM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths
Please copy and paste in the commands you are using, and the output.
I suspect you have made your box bigger, but it still contains the same
number of molecules and you still have pressure coupli
Subject: RE: [gmx-users] the box lengths
>
>
>
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Justin A. Lemkul [jalem...@vt.edu]
> Sent: Monday, June 14, 2010 10:02 PM
> To: Gromacs Users' Lis
#ZHAO LINA# wrote:
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths
#ZHAO
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 10:02 PM
To: Gromacs Users' List
Subject: Re: [gmx-users] the box lengths
#ZHAO LINA#
#ZHAO LINA# wrote:
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths
___
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Justin A. Lemkul [jalem...@vt.edu]
Sent: Monday, June 14, 2010 9:33 PM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] the box lengths
#ZHAO LINA# wrote:
>
#ZHAO LINA# wrote:
Hi,
First time I meet this problem,
ERROR: One of the box lengths is smaller than twice the cut-off length.
Increase the box size or decrease rlist.
I just followed the advice increase the box size, I tried twice in the
editconf about the box size, actually this box is re
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