Dear all
My system consists of protein and CNT. I know I can calculate
Interaction energy and interface area using g_energy and g_sas tools,
respectively.
I want to obtain Interaction energy of my system as a function of the
interface area between the protein and CNT.
How to do this?
Any help
step-by-step
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 9:51 AM, maryam haji maryam6...@gmail.com wrote:
Dear all
My system consists of protein and CNT. I know I can calculate
Interaction energy and interface area using g_energy and g_sas tools,
respectively.
I want to obtain
Dear GROMACS users,
I am new to GROMACS, and recently started using the version 4.6.5.
I have seen a lot of NPT related issues raised earlier in this forum, but in
my case the error looks much more severe.
I am following Justin Lemkul's tutorial
Dear GROMACS users,
I am new to GROMACS, and recently started using the version 4.6.5.
I have seen a lot of NPT related issues raised earlier in this forum, but
in my case the error looks much more severe.
I am following Justin Lemkul's tutorial (
On 2/23/14, 3:51 AM, maryam haji wrote:
Dear all
My system consists of protein and CNT. I know I can calculate
Interaction energy and interface area using g_energy and g_sas tools,
respectively.
I want to obtain Interaction energy of my system as a function of the
interface area between the
On 2/23/14, 8:30 AM, sujith wrote:
Dear GROMACS users,
I am new to GROMACS, and recently started using the version 4.6.5.
I have seen a lot of NPT related issues raised earlier in this forum, but in
my case the error looks much more severe.
I am following Justin Lemkul's tutorial
On 2/23/14, 10:43 AM, Marcelo Depólo wrote:
Hey,
I am running this 1000ns simulation but for some reason mdrun is backing up
the data in multiple files (.edr.1# - .edr.9#, for instance).
Is it a normal behavior?
No, that means rather than launching a parallel mdrun process, you're
On 2/23/14, 10:36 AM, sojovictor wrote:
Dear all,
I would like to find the difference in the energy of binding or insertion of
a protein into two different types of phospholipid membranes (plus water and
ions). i.e., my hypothesis is that the energy should be lower with one type
of membrane
But it is not quite happening simultaneously, Justin.
It is producing one after another and, consequently, backing up the files.
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On 2/23/14, 11:00 AM, Marcelo Depólo wrote:
But it is not quite happening simultaneously, Justin.
It is producing one after another and, consequently, backing up the files.
You'll have to provide the exact commands you're issuing. Likely you're leaving
the output names to the default,
Thanks, Justin! That's really helpful indeed.
You are correct, I want to know what's the energy change in replacing one
lipid with the other, hypothesising that going to the wrong lipid will
imply an energetic cost.
Via umbrella sampling, I would thus:
1) Set up a full system with protein,
are you sure that your binary is parallel?
how many frames do those trajectory files contain?
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 5:32 PM, Marcelo Depólo marcelodep...@gmail.com wrote:
Maybe I should explain it better.
I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o
Pretty sure. I ran other simulations in the same system and worked just
fine.
About the frames, each file contains different number of frames, apparently
random numbers (one file contains 400ns of data and other contains 10ns)
2014-02-23 17:54 GMT+01:00 Dr. Vitaly Chaban vvcha...@gmail.com:
On 2/23/14, 11:32 AM, Marcelo Depólo wrote:
Maybe I should explain it better.
I am using *mpirun -np 24 mdrun -s prt.tpr -e prt.edr -o prt.trr*, pretty
much a standard line. This job in a batch creates the outputs and, after
some (random) time, a back up is done and new files are written, but
On 2/23/14, 11:54 AM, sojovictor wrote:
Thanks, Justin! That's really helpful indeed.
You are correct, I want to know what's the energy change in replacing one
lipid with the other, hypothesising that going to the wrong lipid will
imply an energetic cost.
Via umbrella sampling, I would thus:
Normally an MPI-enabled mdrun would be named mdrun_mpi, and running a
non-MPI mdrun would produce symptoms like yours depending exactly how your
filesystem chooses to do things, so Justin and Vitaly's theory is sound.
Look at the top section of your .log file for what mdrun thinks about MPI!
Mark
Or the TNG format, supported in upcoming GROMACS 5.0, VMD sometime soon,
and in its own API. TNG has state-of-the-art compression of coordinates
*and* good single-file metadata.
Mark
On Sun, Feb 23, 2014 at 1:35 PM, ABEL Stephane 175950
stephane.a...@cea.frwrote:
Thanks Vitaly and Marks for
On 2/23/14, 12:10 PM, Marcelo Depólo wrote:
Pretty sure. I ran other simulations in the same system and worked just
fine.
About the frames, each file contains different number of frames, apparently
random numbers (one file contains 400ns of data and other contains 10ns)
What are the
Still about the question of temperature coupling with method of the
periodic perturbation I have the following question: Only the y and z
components are rescaled in the temperature coupling?
Original Post:
I am trying to calculate the viscosity of water (spc model) by
periodic perturbation
Justin, as far as I realized, the next log file starts at 0ps what would
mean that it is re-starting for some reason. At first, I imagined that it
was only splitting the data among files due to some kind of size limit, as
you said, but when I tried to concatenate the trajectories, it gives me a
I believe you are now posing the questions, where you are expected to
open the source code yourself and read...
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 8:25 PM, Marcelo Vanean vanea...@gmail.com wrote:
Still about the question of temperature coupling with method of the
periodic
Hi,
Unfortunately, there is a fair bit of code in GROMACS that only the author
understands (if that many). Do have a look for any primary literature e.g.
cited from the manual. But you may need to identify and read the relevant
code fragment, unless you can devise a test of whether your
Hello,
Thank you both for the comments. I am using gromos96 forcefield . I read
a little bit and as you said the nonbonded cutoff has to be higher.
The tau_p=5ps was chosen , since the manual mentions that the value has to
be raised by 4-5 times on going from berendsen to parrinello-rahman
Hello,
Thank you both for the comments. I am using gromos96 forcefield . I read
a little bit and as you said the nonbonded cutoff has to be higher.
The tau_p=5ps was chosen , since the manual mentions that the value has to
be raised by 4-5 times on going from berendsen to parrinello-rahman
Dear members,
I am trying to run REMD simulation for poly Alanine (12 residue) system. I used
remd generator to get the range of temperature with the exchange probability of
0.3. I was getting the 125 replicas. I tried to simulate 125 replicas its
drastically slow down the simulation time (for
Because every replica has to be calculated separately, it seems the speed
is not that slow (125 * 0.07 ~ 9 ns).
Also, to evaluate it, you should post how many CPUs you used, and other
information like exchange attempt frequency...
Francis
On Mon, Feb 24, 2014 at 3:32 PM, Singam Karthick
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