[gmx-users] the box lengths

[#ZHAO LINA#]

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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of #ZHAO LINA# [ZHAO0139 at 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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on behalf of Dallas B. Warren [Dallas.Warren at 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.warren at 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-bounces at gromacs.org [mailto:gmx-users-
> bounces at 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-bounces at gromacs.org [gmx-users-bounces at gromacs.org] on
> behalf of Dallas B. Warren [Dallas.Warren at 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.warren at 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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