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

[Carl-Johan Högberg]

Hi

Now i have changed the values för -box but the problem is still there. 
At the end of the error message it says:
-----
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.
-----

And then:

-----
Fatal error: ci = -1 should be in 0 .. -1 [FILE nsgrid.c, LINE 218]
-----

For completness i attach my .mdp file:
-----
title                    = Yo
cpp                      = /lib/cpp
include                  = -I/usr/local/gromacs/share/top
define                   =
integrator               = md
dt                       = 0.002
nsteps                   = 1000
nstxout                  = 100
nstvout                  = 100
nstlog                   = 100
nstenergy                = 250
nstxtcout                = 250
xtc_grps                 = dmpc  SOL
energygrps               = dmpc  SOL
nstlist                  = 10
ns_type                  = grid
rlist                    = 0.8
coulombtype              = cut-off
rcoulomb                 = 1.4
rvdw                     = 0.8
tcoupl                   = Berendsen
tc-grps                  = dmpc  SOL
tau_t                    = 0.1  0.1
ref_t                    = 300  300
Pcoupl                   = Berendsen
tau_p                    = 1.0
compressibility          = 4.5e-5
ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = none
-----

Best regards
Calle




Tsjerk Wassenaar wrote:

>
> Hi,
>
> You should consider that distances in pdb files are in angstrom, 
> whereas in Gromacs they are in nm.
> So instead of using -box 61.760 61.760 66.608 you should use -box 
> 6.1760 6.1760 6.6608
>
> Greetings,
>
> Tsjerk
>
> Carl-Johan Högberg wrote:
>
>> 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
>> -----
>
>
>
>


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