Hi Gromacs users,
I was trying to compute minimum distance between groups in a cubic water box
with g_mindist using periodic boundary condition. In order to test this, I
added one more "atom" which is far away from any of the other atoms in the
pdb file. The mindist between that atom and all the w
The box is 24X24X24 (Angstrom). The dummy atom I added at the end is about
31 A away from the closest water in the box. But if it is periodic,
shouldn't there be waters near the dummy too?
On Wed, Mar 3, 2010 at 10:29 PM, Mark Abraham wrote:
> On 4/03/2010 11:30 AM, Dian Jiao wrote:
you using? Can you assert that the pdb
> file has the correct box? It should have a line starting with CRYST1
> (grep "^CRYST1" file.pdb). Some versions of gromacs (3.3.2 I think)
> didn't write the CRYST1 record, and thus disallow PBC related
> operations.
>
>
pdb format at www.rcsb.org/pdb
>
> Hope it helps,
>
> Tsjerk
>
> On Thu, Mar 4, 2010 at 6:04 PM, Dian Jiao wrote:
> > Hi Tsjerk,
> >
> > My gromacs is 4.0.4.
> >
> > As it turns out, I do not have a CRYST1 keyword in my pdb file, so I
> guess
> &g
I was following the instruction to install gromacs 4.0.6 on my machine.
./configure --enable-threads --enable-float --enable-sse --prefix=[mypath]
make
make install
The configure looks ok but no Makefile is generated. When I do make or make
install, it gives me the error:
make: *** No targets sp
Actually, I tried 4.0.7 first from this link,
http://www.gromacs.org/index.php?title=Download_%26_Installation
It didn't work (same error). That's why I downloaded 4.0.6 from the same
webpage.
On Fri, Mar 5, 2010 at 10:51 AM, Justin A. Lemkul wrote:
>
>
> Dian Jiao wrote:
&
I got it to work finally. Didn't install fftw earlier. Thanks.
On Fri, Mar 5, 2010 at 4:02 PM, Mark Abraham wrote:
> On 6/03/2010 5:05 AM, Dian Jiao wrote:
>
>> Actually, I tried 4.0.7 first from this link,
>> http://www.gromacs.org/index.php?title=Download_%26_Installati
Hi gmx users,
I was running g_mindist as a batch job for a big number of files on a pbs
cluster. The huge amount of output was redirected to the error file which
has a size limit. Is there way to discard the output of g_mindist. I tried
/dev/null as below, it didn't work.
g_mindist -f tra.pdb -n
Thank you, Justin.
On Mon, Mar 8, 2010 at 6:22 PM, Justin A. Lemkul wrote:
>
>
> Dian Jiao wrote:
>
>> Hi gmx users,
>>
>> I was running g_mindist as a batch job for a big number of files on a pbs
>> cluster. The huge amount of output was redirected to the
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