Dear all,
I am trying to use g_cluster protocol to get representative snapshots of
the simulations. I have concatenated 9 set of simulations and run g_cluster
for the same. The result shows a total of 198 clusters.
Is this correct?
Following is the command I have used:
g_cluster -s models.gro -
Hi Sapna,
How should we know how many clusters you should have?
A cutoff of 0.2 is quite tight, and will give many clusters. Whether that's
what you want/need or whether that's meaningful/helpful for your goals is
something you should consider. We don't know what you're trying or doing.
Cheers,
Dear Mark,
I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom
system. What further could be done?
Kind Regards,
Antara
--
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Systems biology group
CSIR-Institute of Genomics & Integrative Biology
South Campus
New Delhi - 110020
M : +91-9717970
Hello,
how can I find out the tpx version of a tpr file?
Cheers
Sabine
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I'm looking to generate the topology of a HEM protein , I choose CHARMM as a
force field. At the begining, when I run pdb2gmx I had this error about missing
hydrogen's:
WARNING:
atom HA is missing in residue HEM 473 in the pdb file
You
might need to add atom HA to the hydrogen database
Hi,
Mdrun reports it to the log file, or likely gmx dump and gmx check also do
so.
Mark
On Mon, 23 May 2016 11:12 Sabine Reisser wrote:
> Hello,
>
> how can I find out the tpx version of a tpr file?
>
> Cheers
> Sabine
> --
> Gromacs Users mailing list
>
> * Please search the archive at
> http
Hi,
Justin suggested confirming with gmx check. Since we know the file is
large, find out what your file system is, or try another machine.
Mark
On Mon, 23 May 2016 10:50 Antara mazumdar wrote:
> Dear Mark,
>
>I checked the file size , MD.trr is 3.2 Terabytes. It is a million atom
> system
Hey :)
If you just have the .tpr and you don't want to use Gromacs' tools, you can
use python:
python -c 'import struct; print
"".join(struct.unpack(100*"c",open("YOUR-TPR-HERE").read(100)))'
(Python 2, mind you).
Cheers,
Tsjerk
On Mon, May 23, 2016 at 11:33 AM, Mark Abraham
wrote:
> Hi,
>
Thanks, that works.
The log file has only the mdrun version. Only if executable and tpr file
version differ, there's a note. Same with gmx dump and check.
Cheers
Sabine
On 05/23/2016 11:39 AM, Tsjerk Wassenaar wrote:
Hey :)
If you just have the .tpr and you don't want to use Gromacs' tools,
Dear Users:
I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
The link provided in the gromacs website (Removing a GROMACS installation)
does not give any solution with the same.
how can i uninstall gromacs 5.0 ??
Thanks in advance.
Anurag Dobhal
--
*DISCLAIMER:*
*This comm
Hi Everyone,
I want to model the substrate specificity of an enzyme (lipase). I have
created a mutant which has specificity toward some fatty acid (long chain
unsaturated). I want to analyze the reason behind it. I have done the
following things please let me know if I am going wrong anywhere. Plea
Hi,
You can run "make uninstall" from your build directory (as root), but I
don't know how good a job that really does. If you've installed to the
default location of /usr/local/gromacs then you can also just delete that
(as root). Or just don't bother uninstalling (you might want it later!) and
i
Hello Everyone,
I received an error (shown below) while trying to run "Adding ion" step
during
Protein-membrane simulation. Any advice or suggestions will be greatly
appreciated.
The steps utilized proior to "Adding Ions" are mention below:
> pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro
Hi,
sun, that is not the name of any apt-supported GROMACS package that I know
of...
Mark
On Mon, May 23, 2016 at 6:17 PM sun wrote:
> sudo apt-get uninstall Gromacs-5.0
>
>
>
> Sent from my iPhone
>
> > On 23-May-2016, at 6:51 pm, Anurag Dobhal <
> anurag.dob...@nano-medicine.co.in> wrote:
>
sudo apt-get uninstall Gromacs-5.0
Sent from my iPhone
> On 23-May-2016, at 6:51 pm, Anurag Dobhal
> wrote:
>
> Dear Users:
>
> I want to uninstall gromacs 5.0 and replace it with gromacs 5.1.
> The link provided in the gromacs website (Removing a GROMACS installation)
> does not give any
Hi,
You didn't finish writing this email, but I'll bet lunch that you didn't
update the top file like the tutorial suggested :-)
Mark
On Mon, 23 May 2016 17:48 BIJENDRA KHADKA wrote:
> Hello Everyone,
> I received an error (shown below) while trying to run "Adding ion" step
> during
> Protein-
I am so sorry Mark
It sudo apt-get remove Gromacs :)
I used this in Ubuntu. Also, for Gromacs and its dependencies:
sudo apt-get remove --auto-remove gromacs
I hope this works
Sent from my iPhone
> On 23-May-2016, at 9:49 pm, Mark Abraham wrote:
>
> Hi,
>
> sun, that is not the name of any a
Running make uninstall also works
Sent from my iPhone
> On 23-May-2016, at 9:49 pm, Mark Abraham wrote:
>
> Hi,
>
> sun, that is not the name of any apt-supported GROMACS package that I know
> of...
>
> Mark
>
>> On Mon, May 23, 2016 at 6:17 PM sun wrote:
>>
>> sudo apt-get uninstall Groma
I am sorry for so many e-mails but check this link:
http://installion.co.uk/ubuntu/vivid/universe/g/gromacs/uninstall/index.html
Sent from my iPhone
> On 23-May-2016, at 9:49 pm, Mark Abraham wrote:
>
> Hi,
>
> sun, that is not the name of any apt-supported GROMACS package that I know
> of...
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