On 9/18/17 4:18 PM, gangotri dey wrote:
Hello!
I would save it in vmd all at once but I would like to ideally save it in
separate files. Also, the trajconv statement did not work.
Your original error will be solved by passing a .tpr file to trjconv -s,
as suggested below. If you want to s
First off, don't change the cutoff without being sure of what you're doing!
There is one thing you can try: lowering nstlist, the neighbor search
frequency; this is a free parameter and it is picked heuristically. A
larger value will reduce the cost of search but as it will increase
the Verlet buf
Hello!
I would save it in vmd all at once but I would like to ideally save it in
separate files. Also, the trajconv statement did not work.
*Thank you*
*Gangotri *
On Mon, Sep 18, 2017 at 3:08 PM, R C Dash wrote:
> Open you the gro file in VMD. Add load data and show the trr or xtc file
Hi Szilárd,
{I had to trim the message as my message is put on hold because only 50kb
allowed and this message has reached 58 KB! Not due to files attached as
they are shared via dropbox}; Sorry seamless reading might be compromised
for future readers.
Thanks for your replies. I have shared log f
Is there something that I can do without reducing the cut off..?
On Mon, 18 Sep 2017 at 10:27 PM, Szilárd Páll
wrote:
> It means that there is a certain amount of time the CPU and GPU can
> work concurrently to compute forces after which the CPU waits for the
> results from the GPU to do the int
Dear all,
I am attempting to find the Vibrational density of states of protein bound to
ligand in a water box using the command g_dos. To do so, should I extract the
protein part from the entire trajectory file containing coordinates and
velocities of all atoms (trr file) and then run g_dos on
Dear all,
I would like to transform my trajectory file n.trr or n.xtc to n.gro after
my production run. I have used trjcat and trjconv to transform it using the
index file. But in both the cases, it says "Can not write a gro file
without atom names". How can I transform it please?
*Thank you*
It means that there is a certain amount of time the CPU and GPU can
work concurrently to compute forces after which the CPU waits for the
results from the GPU to do the integration. If the CPU finishes a lot
sooner than the GPU, the run will be GPU performance-bound (and
vice-versa) -- which is wha
I receive the following note while doing NVT & NPT.
What does it exactly mean?
I am using charmm36 ff and as per documentation it is necessary to ahve cut
off as 1.2. How can I overcome this note.?
NOTE: The GPU has >20% more load than the CPU. This imbalance causes
performance loss, cons
On Fri, Sep 15, 2017 at 1:06 AM, gromacs query wrote:
> Hi Szilárd,
>
> Sorry this discussion is going long.
> Finally I got one node empty and did some serious tests specially
> considering your first point (discrepancies in benchmarking comparing jobs
> running on empty node vs occupied node). I
>>> However, note that if you are sharing a node with others, if their jobs
> are not correctly affinitized, those processes will affect the performance
> of your job.
>
> Yes exactly. In this case I would need to manually set pinoffset but this
> can be but frustrating if other Gromacs users are n
On Thu, Sep 14, 2017 at 1:02 PM, gromacs query wrote:
> Hi Szilárd,
>
> Here are my replies:
>
>>> Did you run the "fast" single job on an otherwise empty node? That might
> explain it as, when most of the CPU cores are left empty, modern CPUs
> increase clocks (tubo boost) on the used cores highe
Hi,
You're not compiling properly for your cluster, which might have different
hardware in different places. Read its docs and talk to your admins.
Mark
On Mon, Sep 18, 2017 at 4:07 AM Vidya R wrote:
> Thank you for your reply.
>
> When I try to run my job in a single processor through qsub co
Dear all,
Is there any way to obtain PMF from; pull = constant force.? I have seen
wham only supports 'umbrella'
When i try to use umbrella my molecule is not travelling through the
channel.
Thanks in advance.
--
Regards,
Nikhil Maroli
--
Gromacs Users mailing list
* Please search the archi
We were trying to solvate a small peptide (octamer) in water to run a 100ns
simulation of it.
In the pdb2gmx step, we have provided -ignh and -ter options (with NH3+ and
COO-) and used the gromos53a6 forcefield. It did not generate any error.
But it is generating a blank coordinate file (.gro). He
Dear Dilip,
The LJ parameters are present in the topology file and the force-field files
included within. So no need to calculate anything, just to locate them in said
files.
Kind regards,
Erik
__
Erik Marklund, PhD, Marie Skłodowska Curie INCA Fellow
Thank you very much for the links!
Best regards,
Mahsa
On Mon, Sep 18, 2017 at 1:30 AM, Dallas Warren
wrote:
> These two images will help you see what is going on:
>
> https://twitter.com/dr_dbw/status/909559339366572032 - shows a
> molecule that appears to be outside the box.
>
> https://twitt
Hello,
with the aim to simulate a shear stress using DEFORM non-equilibrium
option, I need to calibrate the deformations rates of the box (nm ps-1)
against the experimental value characterized for shear stress (10 dyn/cm2 ~
1 pascal).
Therefore, I would like to know what deformations rates set up
Hello,
with the aim to simulate a shear stress using DEFORM non-equilibrium
option, I need to calibrate the deformations rates of the box (nm ps-1)
against the experimental value characterized for shear stress (10 dyn/cm2 ~
1 pascal).
Therefore, I would like to know what deformations rates set up
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