# [gmx-users] pressure scaling.

Gale, Ella ella.gale at imperial.ac.uk
Fri May 12 16:46:06 CEST 2006

```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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