Thanks all, I know what's wrong now.
I forgot to set pbc = xyz earlier.
By the way, is it normal for test failure of the gmxtest? such as
:~/src/gmxtest$ ./gmxtest.pl complex
FAILED. Check files in field
FAILED. Check files in tip4p
FAILED. Check files in water
3 out of 14 complex tests FAILED
Thanks,
lina
________________________________________
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of #ZHAO LINA# [zhao0...@e.ntu.edu.sg]
Sent: Tuesday, June 15, 2010 1:56 PM
To: Discussion list for GROMACS users
Subject: RE: [gmx-users] the box lengths
Well...
There is one line in try2-water.pdb, shows as below
TITLE Protein
REMARK THIS IS A SIMULATION BOX
CRYST1 86.185 86.185 86.185 60.00 60.00 90.00 P 1 1
Do you think something was wrong during
genion -s try2-water.tpr -o try2-water-ions.pdb -conc 0.15 -neutral -pname NA+
-nname CL-
Thanks,
lina
________________________________________
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 1:41 PM
To: Discussion list for GROMACS 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.
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
---------------------------------
When the only tool you own is a hammer, every 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 3:37 PM
> To: Discussion list for GROMACS users
> Subject: RE: [gmx-users] the box lengths
>
> There is none CRYST1 line in the file try2-water-ions.pdb.
>
> Thanks and regards,
>
> lina
> ________________________________________
> 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 1:24 PM
> 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 Parade, Parkville VIC 3010
> dallas.war...@pharm.monash.edu.au
> +61 3 9903 9167
> ---------------------------------
> When the only tool you own is a hammer, every problem begins to
> resemble
> a nail.
> --
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