[gmx-users] RE:problem with downloaded lipid bilayer

[Carl-Johan Högberg]

Hi

I tried this but i dosen´t seems work. In my -pdb file i have the first 
three lines:

-----
HEADER    128 DMPC bilayer
REMARK    THIS IS A SIMULATION BOX
CRYST1   61.760   61.760   66.608  90.00  90.00  90.00 P 1           1
-----

So for editconf i use the following command:

-----
editconf -f dmpc_npat.pdb -o dmpc.gro -box 61.760 61.760 66.608
-----

After this i start the simulation with mdrun:

-----
mdrun -s dmpc.tpr -o dmpc -c dmpc -e dmpc -g dmpc
-----

Now i get the following error message:

-----
Back Off! I just backed up dmpc.log to ./#dmpc.log.2#
Reading file dmpc.tpr, VERSION 3.2 (single precision)

Back Off! I just backed up dmpc.edr to ./#dmpc.edr.2#
starting mdrun 'Pure DMPC bilayer with 128 lipids and 3655 water molecules'
1000 steps,      2.0 ps.

Warning: 1-4 interaction between 691 and 696 at distance larger than 1 nm
These are ignored for the rest of the simulation
turn on -debug for more information

Back Off! I just backed up dmpc.trr to ./#dmpc.trr.2#

Back Off! I just backed up traj.xtc to ./#traj.xtc.2#

Back Off! I just backed up step0.pdb to ./#step0.pdb.2#

Back Off! I just backed up step1.pdb to ./#step1.pdb.3#
Wrote pdb files with previous and current coordinates

Step 2  Warning: pressure scaling more than 1%, mu: 7.50389e+09 
7.50389e+09 7.50389e+09

Back Off! I just backed up step1.pdb to ./#step1.pdb.4#

Back Off! I just backed up step2.pdb to ./#step2.pdb.1#
Wrote pdb files with previous and current coordinates
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.
-----

It seems like almost the same problem.

Calle








John Simms wrote:

>Hi Calle
>I had a similar problem. It was sorted out by stating the box size at the editconf stage ie
>editconf -f xxx -o yyy.gro -box a b c 
>a, b and c are found at the top of the .pdb file
>Hope this helps
>John   
>_______________________________________________
>gmx-users mailing list
>gmx-users at gromacs.org
>http://www.gromacs.org/mailman/listinfo/gmx-users
>Please don't post (un)subscribe requests to the list. Use the 
>www interface or send it to gmx-users-request at gromacs.org.
>
>  
>


-- 
Carl-Johan Högberg
Department of Physical Chemistry
Arrhenius Laboratory
Stockholm University
S-106 91 Stockholm
Sweden
Phone: +46-8-162373