[gmx-users] problems

[Lianqing Zheng]

OK, here is more detail. I have a simulation box of 2.6364x2.3148x3.2127.
However the ranges of atom coordinates are X [-0.3490, 2.326], Y [-0.108,
2.4230], and Z [-0.6410, 3.3190]. It looks that some atoms are out of the
simulation box, but no warning was given from grompp. By the way, the
coordinates of any atom should be within [-L/2, L/2], right?

Can I move the coordinates a little bit to fix this problem?

Thanks!

Lianqing


On Tue, 30 Nov 2004, David wrote:

>On Tue, 2004-11-30 at 10:45 -0500, Lianqing Zheng wrote:
>> Thanks, David. The same configuration runs 100+ ps in DL_POLY, but I'll
>> check again if there are any conversion (from .xyz to pdb to gro)
>> problems.
>> 
>> How about my second question about dihedral potential? Thanks!
>Check with gmxdump
>
>> 
>> Lianqing
>> 
>> On Thu, 25 Nov 2004, David wrote:
>> 
>> >On Wed, 2004-11-24 at 16:30 -0500, Lianqing Zheng wrote:
>> >> Dear GMX-pals,
>> >> 
>> >> I try to run NPT MD simulation of RDX and got a segmentation error for
>> >> non-mpi version and "MPI process rank 0 (n0, p10908) caught a SIGSEGV."
>> >> error for lam/mpi version. This happens when PME is turned on. When I use
>> >> Cut-off, it gets stuck at step 5 and temperature becomes extremely high.
>> >> 
>> >sounds like a bad starting structure.
>> >
>> >> Another  question is about dihedral entries. If there are repeated
>> >> entries, such as:
>> >> 1 2 3 4 1 180.0 10.0 2
>> >> 1 2 3 4 1 180.0  1.0 4
>> >> 
>> >> The results will be summation of these two or only the second? 
>> >> 
>> >> Thanks a lot!
>> >> 
>> >> Lianqing
>> >> 
>> >> 
>> >> _______________________________________________
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>> >-- 
>> >David.
>> >________________________________________________________________________
>> >David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>> >Dept. of Cell and Molecular Biology, Uppsala University.
>> >Husargatan 3, Box 596,          75124 Uppsala, Sweden
>> >phone:  46 18 471 4205          fax: 46 18 511 755
>> >spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>> >
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>-- 
>David.
>________________________________________________________________________
>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
>Dept. of Cell and Molecular Biology, Uppsala University.
>Husargatan 3, Box 596,          75124 Uppsala, Sweden
>phone:  46 18 471 4205          fax: 46 18 511 755
>spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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