[gmx-users] pressure scaling.

[karamyog singh]

i just removed the problem. the atoms were too close to each other. i have
increased the system size. moreover i used trjconv to center the atoms. the
solution was there in the previous posts. anyway thnx for your help.

have a nice day!

On 5/12/06, Gale, Ella <ella.gale at imperial.ac.uk> wrote:
>
>  I guess that because it's outside the box perhaps, you have coordinates
> that are bigger than the box vectors, if gromacs is clever enough to wrap it
> round they could overlap and overlapping atoms (or atoms too close) can
> cause this. I posted a question about a very similar problem yesterday.
>
> Not sure if that will help.
>
> Ella Gale
>
>
>
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org on behalf of karamyog singh
> Sent: Fri 5/12/2006 2:16 PM
> To: gmx-users at gromacs.org
> Subject: [gmx-users] pressure scaling.
>
> hallo gromaxers, i am new to gromacs and i am facing another problem. I
> got
> the following error when i tried to simulate a dilute gas. I tried
> removing
> pbc but then the run hangs. i even tried changing my box vectors to
> satisfy
> the triclinic conditions.
>
> moreover when i view my initial structure using ngmx. the structure doesnt
> lie in the box completely. its to the left. i think i need to change the
> center of the box for that. am i right?
>
> i have used arbit positions in the conf.gro file. Is this going to hamper
> my
> run in any way? i believe since i am trying to simulate a gas, i can use
> arbit positions. also i am using only 64 atoms. my co-ordinates are all
> positive and less than 1(0.001 to 0.999). my box vectors are 1.920   1.870
> 1.655   0.000   0.000   0.950   0.000   0.950   0.800.
> if any other detail is required please let me know.
>
> how do i reduce pressure scaling? and how can i fix pbc for my cell?
> -
> karamyog.
>
> ---------------------------------
> ERROR :-
> ---------------------------------
>
>  step 0
> Step 1  Warning: pressure scaling more than 1%, mu: 8.68552e+18
> 8.68552e+18
> 8.68552e+18
>
> Step 2  Warning: pressure scaling more than 1%, mu: 3.43938e+19
> 3.43938e+19
> 3.43938e+19
> Warning: Only triclinic boxes with the first vector parallel to the x-axis
> and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Warning: Only triclinic boxes with the first vector parallel to the x-axis
> and the second vector in the xy-plane are supported.
>          Box (3x3):
>             Box[    0]={         nan,          nan,          nan}
>             Box[    1]={         nan,          nan,          nan}
>             Box[    2]={         nan,          nan,          nan}
>          Can not fix pbc.
> Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
>
>
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