[gmx-users] problem regarding pbc
N.Goga at rug.nl
Wed Jan 24 13:30:57 CET 2007
Your problem is met also when we tried to install
gromacs3.3. The administrator pf the HPC cluster tries to
find a solution. If not, I will fix a meeting with him.
Between I might try myself some other variants.
On Wed, 24 Jan 2007 09:45:02 +0100
"Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:
> Hi Sangeeta,
> To start with, you don't really describe a problem
>regarding pbc, as
> you've stated in the subject. Please make the subject
> problem or question directly. This will make it easier
>on the repliers
> on this list to check whether they can be of any help.
>Most of us
> read/discard messages based on the subject.
> Now, you have three questions, which you've stated
> apparently the answers were not informative enough. To
>start with the
> pbc, gromacs uses pbc unless explicitly stated
>otherwise, by adding
> pbc=no in the .mdp file.
> Regarding the chlorides, I think you caught that you
>have to have an
> #include statement in the .top file, reading #include
> next thing to make sure is that the name you've used for
> ions in the .top file matches those in the file ions.itp
> the force field you are using. It may be CL, Cl, Cl-.
>You can try
> either or you can check the file ions.itp in your
> $GMXDIR/share/gromacs/top directory.
>Finally, regarding dssp, please explain what you tried to
> which command you've issued. Note that the file you
> merely a temporary file.
> Hope it helps,
> On 1/24/07, sangeeta <sangeeta at bic.boseinst.ernet.in>
>> Dear GROMACS list members,
>> I have three questions,
>> My protein has +2 charge, so I added two Cl atoms
>>through the program
>> genion and subsequently edited the topol.top file, in
>>spite of that while
>> running mdrun it gave an error that "FATAL error, CL
>>atom type can not be
>> found",I can not understand the problem.
>> I wanted to include PBC in my simulation, I want to
>>know that does
>> Gromacs by default use the option by minimum image
>>convention or we have to
>> edit pr.mdp & md.mdp by writing PBC=xyz ,How can I know
>>that PBC is
>> being included in my simulation?
>> In spite of having dssp and running it I can not get
>>the .xpm files.
>> Instead while dssp is going on some kind of files namely
>> are being produced.How can I generate those xpm files?
>> Waiting for your reply.
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> Tsjerk A. Wassenaar, Ph.D.
> Junior UD (post-doc)
> Biomolecular NMR, Bijvoet Center
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> The Netherlands
> P: +31-30-2539931
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