[gmx-users] problem regarding pbc

[N.Goga]

Tsjerk,

  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.

best regards
Nicu
   


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 
>reflect your
> 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 
>before, but
> 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 
>"ions.itp". The
> next thing to make sure is that the name you've used for 
>your chloride
> ions in the .top file matches those in the file ions.itp 
>listed for
> 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 
>do, i.e.
> which command you've issued. Note that the file you 
>mentioned is
> merely a temporary file.
> 
> Hope it helps,
> 
> Tsjerk
> 
> On 1/24/07, sangeeta <sangeeta at bic.boseinst.ernet.in> 
>wrote:
>>
>> 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 
>>ddEZ117f ddOWnvlx
>> are being produced.How can I generate those xpm files?
>>     Waiting for your reply.
>>
>> regards
>> SANGEETA
>>
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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
>F: +31-30-2537623
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