Hi Nhat,
enjoy and cam down :))
On Wed, Apr 2, 2014 at 10:02 PM, Ly Minh Nhat wrote:
> It WORKS! It really works. Oh my god, thank you so much. Thank you Justin
> Lemkul and Mirco Wahab. Thank you very much. Thank you for spending your
> time to help me, I know that you are busy and I'm appreci
On Apr 3, 2014 1:46 AM, "Amjad Farooq" wrote:
>
> Justin,
>
> I am trying to set up a single system image using PC as the master node
and
> two workstations as slave nodes (essentially a supercompuer; more nodes
> will be added later), so that I can have everything together, instead of
> running m
On 4/2/14, 6:29 PM, Amjad Farooq wrote:
Justin,
I am trying to set up a single system image using PC as the master node and
two workstations as slave nodes (essentially a supercompuer; more nodes
will be added later), so that I can have everything together, instead of
running my simulations in
On Apr 2, 2014 10:26 PM, "Amjad Farooq" wrote:
>
> I have nothing to compare to!
You would have, if you were parallelizing over both machines (which would
usually be a waste of time). You didn't tell us you were only doing I/O
transfer.
> Well, I could run the same simulaton directly
> on the wo
Justin,
I am trying to set up a single system image using PC as the master node and
two workstations as slave nodes (essentially a supercompuer; more nodes
will be added later), so that I can have everything together, instead of
running my simulations individually on each workstation. But, all nod
Thank you, Vitaly!
On Wed, Apr 2, 2014 at 3:49 PM, Dr. Vitaly Chaban wrote:
> If you want a simple response, then it is NO.
>
>
>
> Dr. Vitaly V. Chaban
>
>
> On Wed, Apr 2, 2014 at 9:35 PM, Amjad Farooq wrote:
> > I have nothing to compare to! Well, I could run the same simulaton
> directly
Dear Gromacs users/developers,
I have calculated the PMF for extending a polymer chain from a looped
perfectly circular structure where both ends are in close contact to a fully
linear slightly stretched conformation. To do this, I used the targeted MD
utility of grompp with the target fully exten
On 4/2/14, 3:28 PM, Amjad Farooq wrote:
Aldo,
Thank you so very much for your prompt response.
Well, I have my data files on the PC but MD simulations are running on the
remote workstation. So, yes, you are right: it is the file write/transfer
or I/O operation that will be affected.
But, the
On 4/2/14, 12:23 PM, Manuel Azenha wrote:
Dear all,
When I simulate a solution of a drug in water/methanol to study the
self-aggregation, and try to determine the interaction energy between the
drug molecules , I'm getting net positive values whatever the drug. I'm
simply defining the drug g
On 4/2/14, 2:31 PM, pratibha wrote:
Hi all
I have done simulations of my protein in water-cosolvent system (random
initial addition) at 450K. At the end I have used:
trjconv -f *.xtc -s *.tpr -center -pbc whole -o new.xtc
But when I view my trajectory in vmd, I can see extended intramolecular
So, "between" or "intra"?
"extended intramolecular bonds between cosolvent molecules"
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 8:31 PM, pratibha wrote:
> Hi all
>
> I have done simulations of my protein in water-cosolvent system (random
> initial addition) at 450K. At the end I have used:
>
If you want a simple response, then it is NO.
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 9:35 PM, Amjad Farooq wrote:
> I have nothing to compare to! Well, I could run the same simulaton directly
> on the workstation itself. May be I should do that. But, realistically, I
> will have to run t
Are they whole in the .tpr?
Mark
On Wed, Apr 2, 2014 at 8:31 PM, pratibha wrote:
> Hi all
>
> I have done simulations of my protein in water-cosolvent system (random
> initial addition) at 450K. At the end I have used:
> trjconv -f *.xtc -s *.tpr -center -pbc whole -o new.xtc
> But when I view
Why do you think this unphysical?
Mark
On Wed, Apr 2, 2014 at 6:23 PM, Manuel Azenha wrote:
> Dear all,
>
>
>
> When I simulate a solution of a drug in water/methanol to study the
> self-aggregation, and try to determine the interaction energy between the
> drug molecules , I'm getting net pos
I have nothing to compare to! Well, I could run the same simulaton directly
on the workstation itself. May be I should do that. But, realistically, I
will have to run the test simulation for at least a month (with everything
else being equal) to get any meaningful comparison.
Anyway, I am wonderin
Aldo,
Thank you so very much for your prompt response.
Well, I have my data files on the PC but MD simulations are running on the
remote workstation. So, yes, you are right: it is the file write/transfer
or I/O operation that will be affected.
But, the question is by how much? How much is this g
On 02.04.2014 19:14, Amjad Farooq wrote:
I am running Gromacs 5.0-beta on a remote workstation (next door) from my
PC. The two machines are networked via 1-Gigabit PCI-E ethernet cards (on
each machine) and a CAT-6 ethernet cable.
My question is:
Would my MD simulations benefit in terms of speed
The positive values must be expected only if the drugs are ionized...
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 6:23 PM, Manuel Azenha wrote:
> Dear all,
>
>
>
> When I simulate a solution of a drug in water/methanol to study the
> self-aggregation, and try to determine the interaction ener
Thanks!
I hadnt quite put together that the different hardware calculates things in
different orders, giving different results.
On Tue, Apr 1, 2014 at 9:42 AM, Mark Abraham wrote:
> Not so far. You are comparing the results of two different chaotic
> processes - see
> http://www.gromacs.org/Docu
I believe the answer pretty much depends on how large speedup you get
with your present setup. Would you provide this info?
Dr. Vitaly V. Chaban
On Wed, Apr 2, 2014 at 7:14 PM, Amjad Farooq wrote:
> Hi everyone,
>
> I am running Gromacs 5.0-beta on a remote workstation (next door) from my
> P
Hi all
I have done simulations of my protein in water-cosolvent system (random
initial addition) at 450K. At the end I have used:
trjconv -f *.xtc -s *.tpr -center -pbc whole -o new.xtc
But when I view my trajectory in vmd, I can see extended intramolecular
bonds between cosolvent molecules. This
Hi Farooq,
Are the machines working in parallel? I mean, is the simulation running on
both machines? or Are you using your PC just to send and monitoring the
simulation on the workstation? In the former case, you'll see an improvement in
the communication between both machines and speed of sim
Hi everyone,
I am running Gromacs 5.0-beta on a remote workstation (next door) from my
PC. The two machines are networked via 1-Gigabit PCI-E ethernet cards (on
each machine) and a CAT-6 ethernet cable.
My question is:
Would my MD simulations benefit in terms of speed if I were to use
10-Gigabit
Dear all,
When I simulate a solution of a drug in water/methanol to study the
self-aggregation, and try to determine the interaction energy between the
drug molecules , I'm getting net positive values whatever the drug. I'm
simply defining the drug groups in .mdp. Should it be entered some othe
Thank you Mark Abraham and Justin Lemkul. I know that I haven't responded
for a week and it shouldn't be but I come back to say that I have found the
solution. I want to share this link so maybe it will help someone after me.
Thank you so much for spending your time to help me. I'm honestly
appreci
It WORKS! It really works. Oh my god, thank you so much. Thank you Justin
Lemkul and Mirco Wahab. Thank you very much. Thank you for spending your
time to help me, I know that you are busy and I'm appreciate that. There is
no word can describe my feeling now. Thank you. Best wishes for you :D :D :D
On 4/2/14, 9:25 AM, Ahmet yıldırım wrote:
Dear Justin,
I did as you said but I get the following error when I run grompp command.
I don't know where is my mistake. What should I do to solve it?
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, u
Dear Justin,
I did as you said but I get the following error when I run grompp command.
I don't know where is my mistake. What should I do to solve it?
Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
Please see tables fro
On 4/2/14, 12:22 AM, pravin wrote:
Hi,
This happens due to pbc. You can use trajorder to get right structure.
trjconv, not trjorder. The latter performs a very different function.
-Justin
--
==
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein
On 02.04.2014 05:22, Ly Minh Nhat wrote:
It says:
ooker@ooker-Aspire-4741:~$ source /usr/local/gromacs/bin/GMXRC
ooker@ooker-Aspire-4741:~$ which mdrun
/usr/local/gromacs/bin/mdrun
OK, after that, everything should work fine.
If not, there should have been a warning at
the end of the install
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