Here i am providing you the link of protein structure
https://we.tl/X4yEyZq2aR
On Sun, Sep 10, 2017 at 8:59 PM, Justin Lemkul wrote:
>
>
> On 9/10/17 3:27 AM, ISHRAT JAHAN wrote:
>
>> Dear Justin
>> I have used all the commands given in the link provided by you but unable
>> to get the solution.
Hi,
There is a URL in the error message that gives us you some suggestions, but
the primary one is in the message: use fewer nodes. A small simulation
cannot be usefully parallelised over large amounts of hardware.
Mark
On Mon, 11 Sep 2017 08:47 Juriti Rajbangshi wrote:
> Hi,
>
> I ha
Hi,
Change the mdp file and use that file to make a new tpr file and that the
file to run a simulation.
Mark
On Mon, 11 Sep 2017 08:21 Meagha ramana kumar wrote:
> Hi gmx-users,
>
> My problem may sound silly, but please help me with it. I know how to
> change dielectric constant for simulatio
I'm still not sure why would the GPU-accelerated EM runs slower than
the CPU-only run -- unless the GPU in question is at best as fast at
computing nonbonded interactions as the CPU (cores) assigned to the
job.
Have you looked at log files?
--
Szilárd
On Sat, Sep 9, 2017 at 1:33 AM, Alex wrote
Hi,
More threads can help, but unless I miscounted, the number of threads you
started in your previous run was larger than the number of cores (i.e. you
oversubscribed the CPU cores). That will never be beneficial with GROMACS.
The run stats look more reasonable now, but your run still starts wit
On 9/11/17 2:43 AM, ISHRAT JAHAN wrote:
how can i check whether the structure is whole or not in .tpr file? After
trjconv whole stage i got broken structure.
This is beyond just a "broken" structure. No amount of PBC manipulation
will fix this; it's as if the topology wasn't sound and you a
On 9/11/17 2:28 AM, Joel Awuah wrote:
Hi gromacs user,
I want to perform a spectroscopic analysis of amino acids. Is there any
module in gromacs to help
me with that.
Sounds more like a quantum mechanical question, so no, not really.
-Justin
--
==
On 9/11/17 1:53 AM, Yanke Peng wrote:
Hi, Justin, Thanks very much for your advice.
I think I should try a low concentration NaCl to verify if the system has
the chance to be energy minimizated.
Here are the exact commands that I used.
1. solution definition
#water box and topology file genera
Hi,
When I give these two commands
gmx grompp -f mdp/min.mdp -o min -pp min -po min
gmx mdrun -deffnm min
I get this error.
What to do?
Reading file min.tpr, VERSION 5.0.2 (single precision)
tMPI error: tMPI Initialization error (in valid comm)
Thanks,
Vidya.R
--
Gromacs Users mailing lis
On Mon, Sep 11, 2017 at 8:44 AM, Vidya R wrote:
> Hi,
>
>
> When I give these two commands
>
> gmx grompp -f mdp/min.mdp -o min -pp min -po min
> gmx mdrun -deffnm min
>
> I get this error.
>
> What to do?
>
>
>
> Reading file min.tpr, VERSION 5.0.2 (single precision)
> tMPI error: tMPI Initializ
no grompp not gives any warning neither i have used -maxwarn option.
On Mon, Sep 11, 2017 at 5:26 PM, Justin Lemkul wrote:
>
>
> On 9/11/17 2:43 AM, ISHRAT JAHAN wrote:
>
>> how can i check whether the structure is whole or not in .tpr file? After
>> trjconv whole stage i got broken structure.
>
Hi,
Yeah I've never seen that, so I assume it's something weird related to how
GROMACS was originally compiled vs how the system has been updated since.
Since a rebuild is the way to investigate that, definitely update to at
least the latest 5.0.x while you do it.
Mark
On Mon, Sep 11, 2017 at 3:
Hello All,
Can someone please help me get the "dssp" executable? For secondary
structure analysis.
I did this:
rsync -avz rsync://rsync.cmbi.ru.nl/dssp/ /path_to_dssp/
This downloaded all dssp pdb files but no executable. I am doing this
because I got the error on gromacs run.
Fatal error:
DS
Hi,
You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first two
sentences are useful for you ;-)
Mark
On Mon, Sep 11, 2017 at 5:05 PM Deep kumar
wrote:
> Hello All,
>
> Can someone please help me get the "dssp" executable? For secondary
> structure analysis.
>
> I did this:
>
>
Thanks Marc!
On Mon, Sep 11, 2017 at 6:07 PM, Mark Abraham
wrote:
> Hi,
>
> You're reading too far into http://swift.cmbi.ru.nl/gv/dssp/. The first
> two
> sentences are useful for you ;-)
>
> Mark
>
> On Mon, Sep 11, 2017 at 5:05 PM Deep kumar
> wrote:
>
> > Hello All,
> >
> > Can someone plea
Hello All,
I ran a 10ns simulation on a wild and mutant type of a protein complex.
Attached is the rmsf graph. "Green" is the mutant protein with mutation at
residue 71 (marked) and "purple" is the wild protein. After looking at the
graph can it be said that the mutant has made the complex more s
Hi,
Clearly the .mdp file changes you say you are making aren't showing up
later in wherever you are observing a 1.12, but we'll need to see a lot
more detail of your process - e.g. command lines with the file names - to
suggest what might be wrong. That means you need to be able to copy and
paste
Hi, Justin thanks again for your reply!
1. The 352 water molecules in a .gro file was actually gotten. I have
checked it by viewing the .gro file and by the VMD and Avogrado software.
2. Could the failure be caused by the out-of-box hydrogen atoms? (Some of H
atoms are out of the definition box bo
Hello All,
I ran a 10ns simulation on a wild and mutant type of a protein complex.
Attached is the rmsf graph. "Green" is the mutant protein with mutation at
residue 71 (marked) and "purple" is the wild protein. After looking at the
graph can it be said that the mutant has made the complex more s
Hello all,
Is there a way to use the free energy code with position restraints
(similar to the way that the free energy code interacts with the pull
code)? From the manual all I can see that might be relevant is
"restraint-lambdas" but that is apparently only for "dihedral restraints,
and the pull
Hello All,
I ran a 10ns simulation on a wild and mutant type of a protein complex.
Attached is the rmsf graph. "Green" is the mutant protein with mutation at
residue 71 (marked) and "purple" is the wild protein. After looking at the
graph can it be said that the mutant has made the complex more s
Hello GROMACS users,
As Wes had advised previously in this thread, the issue with the vdw
tranformations was rectified by removing the charges from the topology
file. Thereafter, I also tried running free energy calculations using the
following free-energy parameters:
Just to add to the above post, running a none to vdw-q tranformation using
the following parameters also results in the same error for simulation at
first lambda.
*
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